GapOverlap: Difference between revisions

Latest revision as of 19:01, 8 March 2019

methods

The measurements are taken from the gapOverlap.bed[.gz] file in /hive/data/genomes/<db>/bed/gapOverlap/gapOverlap.bed[.gz] The score column in the bed file (column 5) is the size of the duplicated sequence. The gap size between the duplicated sequence is calculated from: end - start + 2 * score

The size of the duplicated sequence is between 30 bases and 1000 bases, we are not checking for sizes outside that range.

The item total is the sum of the sizes of the duplicated sequences. Not both sides though, just one side. This indicates how much sequence is duplicated. Multiply this by 2 to see total amount of sequence involved in these repeats for both sides.

The gap total is the sum of the sizes of all the gaps involved.

table features

The table columns can be sorted, click on the up/down arrow icon in the column header. The 'year' is what we have in the dbDb table as indicated from the assembly information files for the date of the assembly. A few do not have dates (set to 1880), and do not have database genome browsers.

The example item is a worst case example, where the ratio of duplicate sequence size to gap size is the highest, i.e. smallest gap with largest dup size These ends were found by taking 1,000 bases on each side of any run of N's in the sequence, thus any gap, and aligned with the blat command:

 blat -q=dna -minIdentity=95 -repMatch=10 upstream.fa downstream.fa

Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence before the gap and begins exactly at the start of the downstream sequence after the gap.

gapOverlap table statistics

count	year	dbName	ncbiAsmId	assembly method	item count	item median	item total	gap median	gap total	example item dup size, gap size, link	scatter plot dup size vs. gap size
001	2016	CBA_J	GCA_001624475.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	24180	279.5	7933814	26	26736971	999, 1, chr16:100093490-100095488	plot GCA_001624475.1_CBA_J_v1
002	2016	PAHARI_EIJ	GCA_900095145.1	tbd	6365	69	479534	1	675789	1000, 1, chr7:107557946-107559946	plot GCA_900095145.1_PAHARI_EIJ_v1
003	2016	PWK_PhJ	GCA_001624775.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	246352	65	16823451	25	10585326	1000, 11, chrX:47500642-47502652	plot GCA_001624775.1_PWK_PhJ_v1
004	2016	SPRET_EiJ	GCA_001624865.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail genomics v. August-2015; Ragout v. 2.0b	17567	516	8157541	100	12022683	1000, 1, chr10:66049175-66051175	plot GCA_001624865.1_SPRET_EiJ_v1
005	2016	NZO_HlLtJ	GCA_001624745.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	21209	448	8647582	25	14665906	1000, 1, chr10:29328015-29330015	plot GCA_001624745.1_NZO_HlLtJ_v1
006	2016	129S1_SvImJ	GCA_001624185.1	SGA v. 0.9.19; Ragout v. 2.0b	20479	400	7813478	25	15456883	1000, 1, chr15:34994444-34996444	plot GCA_001624185.1_129S1_SvImJ_v1
007	2016	C57BL_6NJ	GCA_001632555.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	24698	97	6239791	25	14404336	992, 1, chr10:109927459-109929443	plot GCA_001632555.1_C57BL_6NJ_v1
008	2016	AKR_J	GCA_001624295.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	18106	335	6717178	25	14468858	1000, 1, chr16:53464467-53466467	plot GCA_001624295.1_AKR_J_v1
009	2016	C3H_HeJ	GCA_001632575.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	19436	307	6287513	26	12931709	1000, 1, chr1:52782023-52784023	plot GCA_001632575.1_C3H_HeJ_v1
010	2016	FVB_NJ	GCA_001624535.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	14811	355	4902432	11	8504942	1000, 1, chr17:22790916-22792916	plot GCA_001624535.1_FVB_NJ_v1
011	2016	WSB_EiJ	GCA_001624835.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	11455	236	3524308	25	10785288	994, 1, chrX:58921651-58923639	plot GCA_001624835.1_WSB_EiJ_v1
012	2016	A_J	GCA_001624215.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	38843	80	6428892	25	14025482	1000, 1, chr17:63064911-63066911	plot GCA_001624215.1_A_J_v1
013	2016	CAROLI_EIJ	GCA_900094665.1	tbd	6469	70	484857	1	599072	945, 1, chr1:145228793-145230683	plot GCA_900094665.1_CAROLI_EIJ_v1
014	2016	LP_J	GCA_001632615.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	18175	98	5185817	25	13674278	997, 1, chr12:42758762-42760756	plot GCA_001632615.1_LP_J_v1
015	2016	BALB_cJ	GCA_001632525.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	15793	363	5543975	25	10053337	999, 1, chr4:59636957-59638955	plot GCA_001632525.1_BALB_cJ_v1
016	2016	DBA_2J	GCA_001624505.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	13245	98	3606947	25	7251641	999, 1, chr10:47277903-47279901	plot GCA_001624505.1_DBA_2J_v1
017	2016	NOD_ShiLtJ	GCA_001624675.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b	36838	172	10515906	26	25076950	1000, 1, chr15:69777938-69779938	plot GCA_001624675.1_NOD_ShiLtJ_v1
018	2016	CAST_EiJ	GCA_001624445.1	SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail Genomics v. August-2015; Ragout v. 2.0b	14714	324	5063290	100	10013826	1000, 1, chr12:100100159-100102159	plot GCA_001624445.1_CAST_EiJ_v1
019	2013	CHM1	GCF_000306695.2	SRPRISM v. 2.4.28-alpha; ARGO v. 0.1	85	86	10897	88	65164	319, 10, chr6:108876987-108877634	plot CHM1
020	2018	GRCm38B	tbd	tbd	3	304	860	6000	57759	477, 1759, chrX_GPS_017319198v1_random:240297-243009	plot GRCm38B
021	2014	acaChl1	GCF_000695815.1	SOAPdenovo v. 1.6	5	170	1250	188	2340	722, 188, KK833582:5976-7607	plot acaChl1
024	2009	ailMel1	GCF_000004335.2	tbd	48	104	10594	1193	82504	75, 1, GL192694.1:348745-348895	plot ailMel1
025	2012	allMis1	GCF_000281125.1	Allpaths v. R41313; manual scaffolding	1151	83	273934	1	74939	999, 1, JH739280:136433-138431	plot allMis1
026	2013	allSin1	GCF_000455745.1	SOAPdenovo v. 1.05	95	125	26114	2265	261774	69, 10, KE696011:2095494-2095641	plot allSin1
027	2013	amaVit1	GCA_000332375.1	Ray software v. 3	10099	81	1392334	172	2756641	492, 13, KB238901:2710-3706	plot amaVit1
028	2013	anaPla1	GCF_000355885.1	SOAPdenovo Release v. 1.03	31	251	10663	1660	94318	99, 1, KB742632:907264-907462	plot anaPla1
029	2014	ancCey1	GCA_000688135.1	Velvet v. 1.2.05; BGI GapCloser v. 1.12 (release_2011); HaploMerger v. 20111230; ERANGE v. 3.2	805	154	171926	1	85569	981, 1, JARK01000206v1:43215-45177	plot ancCey1
030	2014	angJap1	GCA_000470695.1	CLC NGS Cell v. 3.2; CLC NGS Cell v. 4.0beta	4539	91	477038	1	610535	588, 1, KI304555:142639-143815	plot angJap1
031	2007	anoCar1	tbd	tbd	20	383.5	8167	537.5	23338	965, 100, scaffold_84:3853690-3855719	plot anoCar1
032	2010	anoCar2	GCF_000090745.1	Arachne v. 3.0.0	25	240	6694	258	26105	318, 100, chr4:54548520-54549255	plot anoCar2
033	2003	anoGam1	tbd	tbd	7	528	3139	1000	21041	1000, 384, chr2L:5019927-5022310	plot anoGam1
034	2006	anoGam3	GCF_000005575.2	tbd	6	415	2611	1884.5	20042	1000, 384, chr2L:5538027-5540410	plot anoGam3
035	2017	aotNan1	GCF_000952055.2	PBJelly2 v. 14.9.9; AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2	2334	182.5	863402	100	2688526	990, 10, NW_018504266v1:1888714-1890703	plot aotNan1
036	2013	apaSpi1	GCA_000385615.1	SOAPdenovo v. 1.0.5	607	61	34340	100	56961	86, 10, KB929338:2579176-2579357	plot apaSpi1
038	2004	apiMel1	tbd	tbd	216	50	12150	10	24454	64, 1, Group14.17:517485-517613	plot apiMel1
039	2005	apiMel2	tbd	tbd	133	50	7371	50	19757	168, 50, Group4:4855105-4855490	plot apiMel2
040	2005	apiMel3	tbd	tbd	199	62	16045	50	27354	198, 50, Group15:1672512-1672957	plot apiMel3
041	2010	apiMel4	GCF_000002195.4	Atlas assembly system v. before 2011	226	52.5	13378	50	24561	167, 50, Group14:1674117-1674500	plot apiMel4
042	2008	aplCal1	tbd	tbd	25	77	3383	100	16863	390, 100, scaffold_1802:24095-24974	plot aplCal1
043	2014	aptFor1	GCF_000699145.1	SOAPdenovo v. 1.6	109	147	26798	1575	323838	779, 98, KL225582:135043-136698	plot aptFor1
044	2015	aptMan1	GCF_001039765.1	tbd	15742	124	4653010	1	3331011	1000, 1, NW_013987125v1:2508272-2510272	plot aptMan1
045	2014	aquChr1	GCA_000696035.1	ABySS v. 1.3.6	4592	43	201248	65	16118238	65, 1, KK850461:8872-9002	plot aquChr1
046	2014	aquChr2	GCA_000766835.1	AllPaths-LG v. August 2013	326	82.5	31349	1	143600	1000, 1, KN265664v1:16826772-16828772	plot aquChr2
047	2013	araMac1	GCA_000400695.1	CLC Genomics Workbench v. 4.9	120	48.5	7929	33	27135	241, 2, KE047968:4314-4797	plot araMac1
048	1880	araTha1	GCF_000001735.3	tbd	1	289	289	60	60	289, 60, chr3:13855281-13855918	plot araTha1
049	2012	ascSuu1	GCA_000298755.1	SOAPdenovo v. 1.04	9	404	3688	555	6481	1000, 247, JH879107v1:69728-71974	plot ascSuu1
051	2013	astMex1	GCF_000372685.1	AllPathsLG v. Jan-2013	1385	78	137888	100	1964877	647, 1, KB872443:19678-20972	plot astMex1
052	2013	balAcu1	GCF_000493695.1	SOAPdenovo v. 16-Mar-2012	211	149	57860	821	371511	926, 15, KI537556:2252563-2254429	plot balAcu1
053	2014	balPav1	GCA_000709895.1	SOAPdenovo v. 1.6	5	270	1303	216	1098	391, 46, KL482982:8685-9512	plot balPav1
054	2014	bisBis1	GCA_000754665.1	MaSuRCA v. 2.1.0	8184	72	712109	100	947641	933, 100, KN265089v1:519297-521262	plot bisBis1
056	2011	bosMut1	GCA_000298355.1	SOAPdenovo v. 1.14	139	83	27917	1274	256420	71, 14, JH880933:479978-480133	plot bosMut1
057	2004	bosTau1	tbd	tbd	6550	40	289123	50	609155	200, 50, SCAFFOLD51732:9156-9605	plot bosTau1
058	2005	bosTau2	tbd	tbd	4361	105	564259	50	2525381	997, 50, scaffold4383:34413-36456	plot bosTau2
059	2006	bosTau3	tbd	tbd	411	51	38673	50	270212	1000, 50, chr10:68862764-68864813	plot bosTau3
060	2007	bosTau4	tbd	tbd	437	53	52814	50	376407	1000, 50, chr10:75537624-75539673	plot bosTau4
061	2009	bosTau5	tbd	tbd	435	53	51742	50	376650	1000, 50, chr10:75464684-75466733	plot bosTau5
062	2009	bosTau6	GCF_000003055.5	UMD Overlapper v. 2009; additional processing	789	670	463109	100	87080	923, 1, chr22:31476636-31478482	plot bosTau6
063	2011	bosTau7	tbd	tbd	413	55	39706	50	141131	1000, 50, chr10:75201034-75203083	plot bosTau7
064	2014	bosTau8	GCF_000003055.5	UMD Overlapper v. 2009; additional processing	789	670	463109	100	87080	923, 1, chr22:31476636-31478482	plot bosTau8
065	2018	bosTau9	GCF_002263795.1	Falcon v. FEB-2016	1	75	75	25	25	75, 25, chr13:11061714-11061888	plot bosTau9
066	2009	bosTauMd3	tbd	tbd	789	670	463109	100	87080	923, 1, chr22:31476636-31478482	plot bosTauMd3
067	2006	braFlo1	tbd	tbd	31	484	14260	417	12668	375, 1, chrUn:879323570-879324320	plot braFlo1
068	2008	braFlo2	tbd	tbd	22	439	8529	411	9064	36, 1, Bf_V2_248:1229532-1229604	plot braFlo2
069	1880	braRap1	GCF_000309985.1	SOAPdenovo v. 1.04	12	104	3193	2810	47557	587, 472, chrUn_JH977260:73788-75433	plot braRap1
070	2007	bruMal1	tbd	tbd	55	50	6093	1	18780	87, 1, Bmal_supercontig14387:293-467	plot bruMal1
071	2014	bruMal2	tbd	tbd	46	124.5	12221	431.5	63506	1000, 20, Bmal_v3_scaffold83:22898-24917	plot bruMal2
072	2013	bubBub1	GCF_000471725.1	MaSuRCA v. 1.8.3	2383	163	395268	100	251657	990, 100, KI418684:2409965-2412044	plot bubBub1
073	2014	bucRhi1	GCF_000710305.1	SOAPdenovo v. 1.6	31	114	5089	78	3263	327, 10, KL526600:8925-9588	plot bucRhi1
075	2011	burXyl1	tbd	tbd	65	601	33110	301	19553	977, 300, scaffold00460:102617-104870	plot burXyl1
076	2010	caeAng1	GCA_000165025.1	Velvet v. 0.7.56	414	41	16726	2	1802	46, 2, scafRNAPATH105:2285-2378	plot caeAng1
077	2012	caeAng2	tbd	tbd	461	46	19505	2	1495	46, 2, Cang_2012_03_13_00008:384957-385050	plot caeAng2
078	2008	caeJap1	tbd	tbd	135	58	10431	186	27893	687, 10, chrUn:37794313-37795696	plot caeJap1
079	2009	caeJap2	tbd	tbd	765	103	130030	1018	891958	707, 10, chrUn:150512438-150513861	plot caeJap2
080	1880	caeJap2a	tbd	tbd	764	103	129273	1018	890958	707, 10, Cjap_Contig4853:3969-5392	plot caeJap2a
082	2010	caeJap4	GCA_000147155.1	Celera assembler v. 6.0	16	98.5	3188	20	1468	1000, 20, Scaffold17129:65445-67464	plot caeJap4
083	2007	caePb1	tbd	tbd	115	44	9160	164	37674	476, 10, chrUn:52430125-52431086	plot caePb1
084	2008	caePb2	tbd	tbd	83	37	3814	222	63681	230, 10, chrUn:74484521-74484990	plot caePb2
085	2010	caePb3	GCA_000143925.2	PCAP v. 9/3/04	89	37	4915	222	74680	230, 10, Scfld02_75:384084-384553	plot caePb3
086	2005	caeRem1	tbd	tbd	58	96	10213	133.5	11238	678, 10, SuperCont3:723391-724756	plot caeRem1
087	2006	caeRem2	tbd	tbd	58	96	10213	133.5	11238	678, 10, chrUn:13919319-13920684	plot caeRem2
088	2007	caeRem3	tbd	tbd	46	50	5760	197.5	14178	460, 10, chrUn:27560772-27561701	plot caeRem3
089	2007	caeRem4	GCF_000149515.1	tbd	46	50	5760	197.5	14178	460, 10, Crem_Contig253:25277-26206	plot caeRem4
090	2010	caeSp111	GCA_000186765.1	Celera assembler v. 6.0	4	194.5	760	20	80	333, 20, Scaffold629:32984714-32985399	plot caeSp111
091	2012	caeSp51	tbd	tbd	14	34	730	12.5	894	201, 3, Csp5_scaffold_09411:792-1196	plot caeSp51
092	2010	caeSp71	tbd	tbd	535	47	30250	213	312209	162, 20, Scaffold11:29462-29805	plot caeSp71
093	2010	caeSp91	tbd	tbd	26	217.5	7172	8745	180575	1000, 20, Scaffold7498:303469-305488	plot caeSp91
094	2014	calAnn1	GCF_000699085.1	SOAPdenovo v. 1.6	89	127	16337	1006	168943	440, 38, KL218155:301090-302007	plot calAnn1
095	2007	calJac1	tbd	tbd	1597	42	129367	182	377725	937, 10, Contig4771:110891-112774	plot calJac1
096	2009	calJac3	GCF_000004665.1	PCAP v. 2009	1516	43	116646	183.5	452860	807, 10, chr3:111956760-111958383	plot calJac3
097	2013	calMil1	GCF_000165045.1	Celera v. 6.1	31	123	8335	100	70257	1000, 100, KI635945:3331497-3333596	plot calMil1
098	2011	camFer1	GCF_000311805.1	SOAPdenovo v. V1.05	11	205	2059	129	2031	237, 2, KB018701:319294-319769	plot camFer1
099	2004	canFam1	tbd	tbd	12	153	2669	210.5	8118	104, 1, chr18:45376349-45376557	plot canFam1
100	2005	canFam2	tbd	tbd	32	199.5	8095	1	5245	746, 1, chrUn:76334072-76335564	plot canFam2
101	2011	canFam3	GCF_000002285.3	Arachne v. April 2010	34	175.5	8234	10	4545	746, 10, chrUn_JH374132:3424-4925	plot canFam3
104	2014	capCar1	GCF_000700745.1	SOAPdenovo v. 1.6	4	105	618	48	354	139, 26, KL359104:23556-23859	plot capCar1
105	2012	capHir1	GCF_000317765.1	SOAPdenovo v. 1.03	627	41	71810	100	546475	988, 16, chr16:40339512-40341503	plot capHir1
106	2014	carCri1	GCF_000690535.1	SOAPdenovo v. 1.6	4	161	644	210.5	878	52, 13, KK509558:67998-68114	plot carCri1
107	2017	casCan1	GCF_001984765.1	ABySS v. 1.9.0; Canu v. 1.2; Platanus v. 1.2.4	19	90	2464	100	1900	952, 100, NW_017870822v1:53223-55226	plot casCan1
108	2014	cavApe1	tbd	tbd	551	47	32236	24	184424	82, 1, AVPZ01000046v1:610580-610744	plot cavApe1
109	2005	cavPor2	tbd	tbd	393	427	164744	100	166667	986, 100, scaffold_291164:123135-125206	plot cavPor2
110	2008	cavPor3	GCF_000151735.1	unknown v. before 2008	3	145	552	100	961	313, 100, scaffold_799:9280-10005	plot cavPor3
111	2002	cb1	tbd	tbd	81	163	20408	145	39126	645, 10, chrUn:51532611-51533910	plot cb1
112	2005	cb2	tbd	tbd	86	153	21033	163.5	42461	645, 10, chrI:9244132-9245431	plot cb2
113	2007	cb3	tbd	tbd	80	148.5	19176	166.5	39580	645, 10, chrI:9355978-9357277	plot cb3
114	2011	cb4	tbd	tbd	86	153	20969	151.5	40114	645, 10, chrI:11247250-11248549	plot cb4
125	2016	cebCap1	GCF_001604975.1	AllPaths-LG v. October 2015	1519	64	128197	1	415272	1000, 1, NW_016107342v1:6176614-6178614	plot cebCap1
126	2015	cerAty1	GCF_000955945.1	AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9	433	92	41269	50	137883	865, 25, NW_012007258v1:11321204-11322958	plot cerAty1
127	2012	cerSim1	GCF_000283155.1	ALLPATHS v. R41370	1818	68	129697	100	270005	815, 100, JH767775:6384924-6386653	plot cerSim1
128	2014	chaVoc1	GCF_000708025.1	SOAPdenovo v. 1.6	47	200	13700	1514	133699	780, 257, KL409415:13594818-13596634	plot chaVoc1
129	2014	chaVoc2	GCF_000708025.1	SOAPdenovo v. 1.6	47	200	13700	1514	133699	780, 257, KL873469:13594818-13596634	plot chaVoc2
130	2013	cheMyd1	GCF_000344595.1	SOAPdenovo v. 1.05	129	204	37111	798	277853	314, 27, KB535131:1778822-1779476	plot cheMyd1
131	2012	chiLan1	GCA_000276665.1	ALLPATHS v. R40776	1183	70	101029	100	267937	996, 100, JH721987:2542897-2544988	plot chiLan1
132	2013	chlSab1	tbd	tbd	23634	81	2123928	10	396229	923, 1, chrX:117110178-117112024	plot chlSab1
133	2014	chlSab2	GCF_000409795.2	ALLPATHS and Newbler v. 13-Feb-2013	23631	81	2123656	10	396199	923, 1, chrX:117110178-117112024	plot chlSab2
134	2014	chlUnd1	GCF_000695195.1	SOAPdenovo v. 1.6	5	293	1223	129	617	310, 65, KK747264:28313-28997	plot chlUnd1
135	2008	choHof1	GCA_000164785.1	tbd	104	54.5	14520	145.5	33892	986, 100, scaffold_56240:3133-5204	plot choHof1
136	2012	chrAsi1	GCF_000296735.1	allpaths v. R42316 HAPLOIDIFY=True	3416	76	339291	100	720504	991, 100, JH823765:402000-404081	plot chrAsi1
137	2011	chrPic1	tbd	tbd	7555	79	738667	50	1230115	64, 1, JH584466:5301285-5301413	plot chrPic1
138	2014	chrPic2	GCA_000241765.2	Newbler v. 2.6	6315	77	629230	206	2593694	1000, 10, chrUn_KK083066v1:1300793-1302802	plot chrPic2
139	2002	ci1	GCA_000183065.1	tbd	28	311.5	8955	50	11060	833, 50, Scaffold_7:289989-291704	plot ci1
140	2005	ci2	tbd	tbd	2	472.5	945	173	346	843, 296, scaffold_403:40134-42115	plot ci2
141	2011	ci3	GCF_000224145.1	tbd	22	258.5	6455	50	9493	597, 50, chrUn_NW_004190451v1:5050-6293	plot ci3
142	2003	cioSav1	tbd	tbd	8	124	1554	100	2755	296, 100, ps_146:263977-264668	plot cioSav1
143	2005	cioSav2	tbd	tbd	6	402.5	2394	200	1668	636, 10, reftig_72:2536022-2537303	plot cioSav2
144	2015	colAng1	GCF_000951035.1	AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2	5690	77	626146	50	1472786	996, 50, NW_012119888v1:35718-37759	plot colAng1
145	2013	colLiv1	GCF_000337935.1	SOAPdenovo v. 2.0	19	116	3824	1290	32865	33, 57, KB379196:2050-2172	plot colLiv1
146	2014	colStr1	GCF_000690715.1	SOAPdenovo v. 1.6	5	161	910	308	1203	362, 113, KK530485:3407-4243	plot colStr1
147	2012	conCri1	GCF_000260355.1	AllPaths v. 2012	1110	72	108033	100	233431	924, 100, JH655880:49229854-49231801	plot conCri1
148	2014	corBra1	GCF_000691975.1	SOAPdenovo v. 1.6	41	90	7520	1445	112176	259, 28, KK718436:193091-193636	plot corBra1
149	2014	corCor1	GCF_000738735.1	AllPaths v. Allpaths-LG version 41687	21	81	2189	1027	27602	81, 1, KL997637:955359-955521	plot corCor1
150	2013	cotJap1	GCA_000511605.1	Soapdenovo v. 1.0.5b; bwa v. 0.5.9; SSPACE v. 1.2	1122	33	38101	68	67651	214, 1, DF262918:84572-85000	plot cotJap1
151	2016	cotJap2	GCF_001577835.1	ALLPATHS-LG v. 4.7.0	628	81	49843	1	166844	808, 1, chr2:125266985-125268601	plot cotJap2
152	2013	criGri1	GCF_000419365.1	SOAPdenovo v. 2.2	588	217	196516	1481.5	1359815	422, 10, KE379019:554914-555767	plot criGri1
153	2011	criGriChoV1	GCF_000223135.1	SOAPdenovo v. 1.05	213	162	53736	1526	472877	369, 10, NW_003615838v1:158557-159304	plot criGriChoV1
154	2017	criGriChoV2	tbd	tbd	9581	199	1595358	100	961598	293, 30, LT883673v1:24540519-24541134	plot criGriChoV2
155	2014	cucCan1	GCF_000709325.1	SOAPdenovo v. 1.6	113	242	41656	972	203191	961, 69, KL448150:311854-313844	plot cucCan1
156	2014	cynSem1	GCF_000523025.1	SOAPdenovo v. April-2011	78	311.5	27891	935.5	165198	568, 38, chr11:13981930-13983103	plot cynSem1
157	2014	cypVar1	GCA_000732505.1	AllPaths v. May 2014	3240	89	423504	1	2210432	1000, 1, KL653732:89449-91449	plot cypVar1
158	2003	danRer1	tbd	tbd	1280	57	186413	10	322061	1000, 10, chr25:16217228-16219237	plot danRer1
159	2014	danRer10	GCF_000002035.5	tbd	575	174	105525	10	17550	484, 10, chr5:1032421-1033398	plot danRer10
160	2017	danRer11	GCF_000002035.6	tbd	127	124	25120	100	12650	42, 1, chr16:27147800-27147884	plot danRer11
161	2004	danRer2	tbd	tbd	1150	58	191859	10	223764	1000, 10, chr10:26174984-26176993	plot danRer2
162	2005	danRer3	tbd	tbd	819	58	88143	10	121196	776, 10, chrUn:112388525-112390086	plot danRer3
163	2006	danRer4	tbd	tbd	726	65.5	121967	14	135012	705, 11, chr25:30060270-30061690	plot danRer4
164	2007	danRer5	tbd	tbd	1559	170	288298	100	155702	73, 1, chr21:35548773-35548919	plot danRer5
165	2008	danRer6	tbd	tbd	1421	133	225674	100	142101	1000, 100, Zv8_scaffold431:54613-56712	plot danRer6
166	2010	danRer7	GCF_000002035.4	tbd	1245	164	217595	100	124500	900, 100, chr22:2241720-2243619	plot danRer7
167	2005	dasNov1	tbd	tbd	55	123	12971	111	31368	681, 100, scaffold_3005:3743-5204	plot dasNov1
168	2008	dasNov2	tbd	tbd	109	136	25865	100	58752	836, 100, scaffold_3394:70496-72267	plot dasNov2
169	2011	dasNov3	GCF_000208655.1	Celera Assembler v. 6.0; Atlas-Link; Atlas-Gap-Fill	239	46	16270	50	94236	677, 50, JH564516:24848-26251	plot dasNov3
170	2014	dicLab1	GCA_000689215.1	tbd	275	423	116519	203	134149	994, 20, HG916850:2956140-2958147	plot dicLab1
171	2008	dipOrd1	GCA_000151885.1	tbd	219	46	46012	379	102683	1000, 100, scaffold_2463:9467-11566	plot dipOrd1
172	2014	dipOrd2	GCF_000151885.1	AllPaths LG v. 41070; Atlas Link v. 2.0; Atlas GapFill v. 2.0	3290	64.5	258868	50	821432	981, 50, NW_012267268v1:6944272-6946283	plot dipOrd2
173	2013	dirImm1	tbd	tbd	505	175	132528	2	32073	999, 1, nDi_2_2_scaf00035:47420-49418	plot dirImm1
174	2003	dm1	tbd	tbd	9	252	2984	20	1237	604, 20, chrU:5250525-5251752	plot dm1
175	2004	dm2	tbd	tbd	8	362	2818	20	1217	604, 20, chrU:5250525-5251752	plot dm2
176	2006	dm3	tbd	tbd	20	286	4907	100	423940	276, 20, chrU:4943122-4943693	plot dm3
177	2014	dm6	GCF_000001215.4	tbd	15	333	4828	100	1340	276, 20, chrUn_DS483709v1:12934-13505	plot dm6
178	2003	dp2	tbd	tbd	113	64	11633	10	9049	784, 10, Contig4969_Contig4496:202614-204191	plot dp2
179	2004	dp3	tbd	tbd	136	79.5	17354	79.5	14988	485, 11, chrU:7044759-7045739	plot dp3
180	2006	dp4	tbd	tbd	183	81	19720	50	18528	798, 50, chrXL_group1e:8376310-8377955	plot dp4
181	2012	droAlb1	GCA_000298335.1	SOAPdenovo v. 1.04	4360	30	131320	22	152454	76, 1, JH853217:889-1041	plot droAlb1
182	2004	droAna1	tbd	tbd	103	252	28853	100	10300	943, 100, 2448822:95133-97118	plot droAna1
183	2005	droAna2	tbd	tbd	32	160	7905	701	72786	791, 25, scaffold_13266:420335-421941	plot droAna2
184	2006	droAna3	GCF_000005115.1	tbd	35	143	8663	671	75001	707, 25, scaffold_13230:483470-484908	plot droAna3
185	2013	droBia2	GCA_000233415.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	14	116.5	2103	20	294	447, 20, KB462730:148150-149063	plot droBia2
186	2013	droBip2	GCA_000236285.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_calland_upgrade.pl v. 1.0	26	103.5	3925	20	520	409, 20, KB464242:790791-791628	plot droBip2
187	2013	droEle2	GCA_000224195.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATKv. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	22	205	4879	20	440	480, 20, KB458480:1051747-1052726	plot droEle2
188	2005	droEre1	tbd	tbd	8	86.5	1545	731	6855	773, 25, scaffold_4784:23686196-23687766	plot droEre1
189	2006	droEre2	GCF_000005135.1	tbd	14	221	4384	239	7433	763, 25, scaffold_4784:18133045-18134595	plot droEre2
190	2013	droEug2	GCA_000236325.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	17	52	1627	20	237	72, 1, AFPQ02002129:815-959	plot droEug2
191	2013	droFic2	GCA_000220665.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	11	352	3277	20	220	424, 20, KB457328:1582-2449	plot droFic2
192	2005	droGri1	tbd	tbd	17	76	2908	444	11143	734, 312, scaffold_24659:1579-3358	plot droGri1
193	2006	droGri2	GCF_000005155.2	tbd	48	60.5	5904	430.5	52107	774, 25, scaffold_15245:16809148-16810720	plot droGri2
194	2013	droKik2	GCA_000224215.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	12	102	1812	20	1721	361, 20, KB458730:24774-25515	plot droKik2
195	2013	droMir2	GCA_000269505.2	Newbler v. 2.6	122	72	16465	10	57520	1000, 10, chr2:9770771-9772780	plot droMir2
197	2005	droMoj2	tbd	tbd	22	219.5	7748	366.5	30847	969, 25, scaffold_6496:4573125-4575087	plot droMoj2
198	2006	droMoj3	GCF_000005175.2	tbd	16	343	6118	426	29359	859, 25, scaffold_6496:14181729-14183471	plot droMoj3
199	2005	droPer1	GCF_000005195.2	tbd	28	402	10502	100	10914	937, 100, super_12:105769-107742	plot droPer1
200	2013	droPse3	GCF_000001765.3	PBJelly v. 12.8.2; Atlas genome assembly	12	51	1309	86	3307	718, 50, chr3:13529933-13531418	plot droPse3
201	2013	droRho2	GCA_000236305.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	35	167	7228	20	1286	454, 20, KB451407:7018-7945	plot droRho2
202	2005	droSec1	GCA_000005215.1	tbd	17	399	6822	100	5318	765, 100, super_59:77146-78775	plot droSec1
203	2005	droSim1	tbd	tbd	109	106	23001	298	40703	801, 10, chr2L:4623692-4625303	plot droSim1
204	2014	droSim2	GCF_000754195.2	Velvet v. 1.1.04	104	58	5999	10	1818	359, 8, chr2R:7425888-7426613	plot droSim2
205	2013	droSuz1	GCA_000472105.1	SOAPdenovo v. 2	71	185	16489	1565	196054	364, 76, KI420423:11753-12556	plot droSuz1
206	2013	droTak2	GCA_000224235.2	Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0	13	102	2070	20	260	472, 20, KB461286:709634-710597	plot droTak2
207	2004	droVir1	tbd	tbd	48	328.5	15839	25	16648	698, 25, scaffold_10:2740496-2741916	plot droVir1
208	2005	droVir2	tbd	tbd	13	232	3421	1415	46365	503, 25, scaffold_13324:149342-150372	plot droVir2
209	2006	droVir3	GCF_000005245.1	tbd	12	341	4206	1536.5	45200	423, 25, scaffold_13324:149231-150101	plot droVir3
210	2006	droWil1	GCF_000005925.1	tbd	23	248	8712	1330	51159	759, 50, scaffold_181150:697726-699293	plot droWil1
211	2006	droWil2	GCF_000005925.1	tbd	23	248	8712	1330	51159	759, 50, CH964291:697726-699293	plot droWil2
212	2004	droYak1	tbd	tbd	65	340	25549	250	24358	955, 50, chrU:40768288-40770247	plot droYak1
213	2005	droYak2	tbd	tbd	99	170	26922	54	37713	684, 10, chr2L:22155365-22156742	plot droYak2
214	2006	droYak3	GCF_000005975.2	tbd	85	143	20479	10	23713	684, 10, chr2L:22155365-22156742	plot droYak3
217	2005	echTel1	tbd	tbd	89	83	17114	100	22024	805, 100, scaffold_272928:13200-14909	plot echTel1
218	2012	echTel2	GCF_000313985.1	ALLPATHS v. R37599	3871	93	620444	100	656358	998, 100, JH980317:1376657-1378752	plot echTel2
219	2014	egrGar1	GCF_000687185.1	SOAPdenovo v. 1.6	112	213.5	33121	1093.5	229589	998, 134, KK502338:445846-447975	plot egrGar1
220	2013	eidHel1	GCA_000465285.1	CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05	27	45	1294	1	186	68, 1, KE769079:2720-2856	plot eidHel1
221	2012	eleEdw1	GCF_000299155.1	allpaths v. R42301 HAPLOIDIFY=True	1643	71	141553	100	311199	1000, 100, JH947463:2106240-2108339	plot eleEdw1
222	2012	eptFus1	GCF_000308155.1	ALLPATHS v. R40371	1641	75	188916	100	378407	988, 100, JH977647:11513546-11515621	plot eptFus1
223	2007	equCab1	tbd	tbd	17	457	5982	100	6200	715, 100, chr2:10720193-10721722	plot equCab1
224	2007	equCab2	tbd	tbd	4	160.5	610	1909	18507	258, 295, chr22:17653073-17653883	plot equCab2
225	2018	equCab3	GCF_002863925.1	Celera Assembler v. 2017; HiRise v. 2017	41	666	24283	1000	38458	949, 20, chr10:36118300-36120217	plot equCab3
226	2014	equPrz1	GCA_000696695.1	SOAPdenovo v. 1.05	39	49	5163	49	12408	78, 11, KK955445:38997-39163	plot equPrz1
227	2006	eriEur1	tbd	tbd	343	435	146738	100	209198	1000, 100, scaffold_366352:52823-54922	plot eriEur1
228	2012	eriEur2	GCF_000296755.1	allpaths v. R41008	3596	70	265454	100	1205265	1000, 100, JH835375:3514396-3516495	plot eriEur2
229	2014	esoLuc1	GCA_000721915.1	AllPaths v. 43500	9785	81	734131	15	1227519	950, 10, LG19:14032217-14034126	plot esoLuc1
231	2015	eulFla1	tbd	tbd	29206	139	4756877	1	60241	986, 1, LGHW01004502v1:47323-49295	plot eulFla1
232	2015	eulMac1	tbd	tbd	41489	62	3147719	53	2639442	393, 1, LGHX01000676v1:768695-769481	plot eulMac1
233	2014	eurHel1	GCF_000690775.1	SOAPdenovo v. 1.6	2	89.5	179	436	872	113, 451, KK569808:53808-54484	plot eurHel1
235	2013	falChe1	GCF_000337975.1	SOAPdenovo v. 1.4	27	206	7614	685	35918	51, 10, KB397780:7020361-7020472	plot falChe1
236	2013	falPer1	GCF_000337955.1	SOAPdenovo v. 1.4	6	48.5	530	631.5	4836	36, 10, KB391040:3398436-3398517	plot falPer1
237	1880	felCat1	tbd	tbd	1343	353	504058	874	2708782	1000, 100, scaffold_217423:45453-47552	plot felCat1
238	2006	felCat3	tbd	tbd	1343	353	504058	874	2708782	1000, 100, scaffold_217423:45453-47552	plot felCat3
239	2008	felCat4	GCA_000003115.1	tbd	9736	503	4582767	10	9398414	1000, 10, chrA2:8725380-8727389	plot felCat4
240	2011	felCat5	GCF_000181335.1	Celera Assembler v. 6.1	27	72	6437	20	100569	488, 20, chrB2:22462351-22463346	plot felCat5
241	2014	felCat8	GCF_000181335.2	CABOG v. 6.2; MaSuRCA assembler v. 8.0; GAA v. 1.0	630	55	50300	10	89447	895, 14, chrB3:27250577-27252380	plot felCat8
243	2013	ficAlb1	GCF_000247815.1	SOAPdenovo v. 1.05	632	77	75592	40.5	206854	982, 1, chr7:28154426-28156390	plot ficAlb1
244	2013	ficAlb2	GCF_000247815.1	SOAPdenovo v. 1.05	632	77	75592	40.5	206854	982, 1, chr7:28154426-28156390	plot ficAlb2
245	2002	fr1	tbd	tbd	76	155.5	19306	50	16684	71, 1, chrUn:149577204-149577346	plot fr1
246	2004	fr2	tbd	tbd	5	313	1682	512	2231	47, 1, chrUn:336404518-336404612	plot fr2
247	2011	fr3	GCF_000180615.1	tbd	6	229	1827	286	2291	47, 1, HE592038:5063-5157	plot fr3
248	2014	fukDam1	GCF_000743615.1	SOAPdenovo v. 1.06	793	203	238200	519	931836	991, 10, NW_011045963v1:25160-27151	plot fukDam1
249	2014	fulGla1	GCF_000690835.1	SOAPdenovo v. 1.6	8	336.5	2583	103.5	1637	450, 20, KK597768:8602-9521	plot fulGla1
250	2010	gadMor1	GCA_000231765.1	tbd	168	53	11363	270	70748	51, 1, CAEA01526699:46-148	plot gadMor1
251	2004	galGal2	tbd	tbd	114	40	12930	124	17674	778, 21, chr3:68417113-68418689	plot galGal2
252	2006	galGal3	tbd	tbd	729	37	34199	500	325853	479, 10, chrUn_random:55035794-55036761	plot galGal3
253	2011	galGal4	GCF_000002315.3	Celera Assembler v. 5.4	55	401	22946	100	31537	805, 100, chr19:3903221-3904930	plot galGal4
254	2015	galGal5	GCF_000002315.4	MHAP/PBcR v. 8.2beta	1	33	33	795	795	33, 795, chrUn_NT_465606v1:9086-9946	plot galGal5
256	2014	galVar1	GCF_000696425.1	SOAPdenovo2 v. April 2014	58964	61	5626241	419	24866346	997, 1, NW_007727116v1:311725-313719	plot galVar1
257	2006	gasAcu1	tbd	tbd	8	46.5	1970	117.5	2520	841, 100, chrUn:38727446-38729227	plot gasAcu1
259	2009	gavGan0	tbd	tbd	30236	134	5187944	5000	145799649	915, 10, scaffold24725:12789-14628	plot gavGan0
260	2014	gavSte1	GCF_000690875.1	SOAPdenovo v. 1.6	5	164	848	318	2312	269, 245, KK640233:828-1610	plot gavSte1
261	2012	geoFor1	GCF_000277835.1	SOAPdenovo v. 2.01	32	105.5	4877	945.5	51025	617, 11, JH739922:1318693-1319937	plot geoFor1
263	2009	gorGor2	tbd	tbd	6585	247	2365617	10	499615	1000, 10, chr10_101645027_418909:206049-208058	plot gorGor2
264	2011	gorGor3	GCF_000151905.1	tbd	6926	246	2475426	10	533805	1000, 10, chr10:101539188-101541197	plot gorGor3
265	2014	gorGor4	GCA_000151905.3	tbd	8691	94	1514940	25	982883	246, 1, chr9:24397320-24397812	plot gorGor4
267	2009	haeCon1	tbd	tbd	25	39	1031	10	1745	58, 10, Hcon_Contig0056815:13389-13514	plot haeCon1
268	2013	haeCon2	tbd	tbd	5378	149	831727	55	351011	700, 1, scaffold_63:260903-262303	plot haeCon2
269	2014	halAlb1	GCF_000691405.1	SOAPdenovo v. 1.6	11	126	1936	370	3807	466, 102, KK641449:26277-27310	plot halAlb1
270	2014	halLeu1	GCF_000737465.1	SOAPdenovo2 v. May 2014	14	280	4342	95	1676	194, 10, KL869356:8708537-8708934	plot halLeu1
271	2011	hapBur1	GCF_000239415.1	ALLPATHS-LG v. R35951	965	95	135908	20	374038	975, 20, JH425754:7557-9526	plot hapBur1
273	2011	hetBac1	GCA_000223415.1	Celera assembler v. 6.0	3	228	1282	20	60	1000, 20, GL996479v1:885362-887381	plot hetBac1
274	2011	hetGla1	tbd	tbd	743	313	285174	1994	2914751	785, 43, JH165660:4306-5918	plot hetGla1
275	2012	hetGla2	GCF_000247695.1	AllPaths v. R39605	595	70	44604	100	201552	1000, 100, JH602085:17402968-17405067	plot hetGla2
276	2009	hg19	tbd	tbd	1	200	200	3000000	3000000	200, 3000000, chrY:10104354-13104753	plot hg19
277	2013	hg38	GCF_000001405.26	tbd	12	78	974	440	56689	125, 20, chrUn_KI270442v1:175618-175887	plot hg38
281	2012	jacJac1	GCF_000280705.1	ALLPATHS v. R41689 HAPLOIDIFY=True	2666	63	196366	100	569918	1000, 100, JH725440:52488719-52490818	plot jacJac1
282	2011	latCha1	GCF_000225785.1	AllPaths v. R36819	2038	77	159059	100	504858	955, 100, JH127253:476850-478859	plot latCha1
284	2014	lepDis1	GCF_000691785.1	SOAPdenovo v. 1.6	1	50	50	229	229	50, 229, KK681583:9399-9727	plot lepDis1
285	2011	lepOcu1	GCF_000242695.1	AllPaths v. R38293	2079	95	232474	100	466733	1000, 100, chrLG4:37780111-37782210	plot lepOcu1
286	2013	lepWed1	GCF_000349705.1	allpaths v. R41856 HAPLOIDIFY=True	2022	63	135843	100	1218867	1000, 100, KB715312:1023296-1025395	plot lepWed1
287	2013	letCam1	GCA_000466285.1	Newbler v. 2.7	1453	69	123952	100	739039	280, 39, KE994354:70338-70936	plot letCam1
288	1880	linHum0	GCF_000217595.1	CABOG v. 5.3	179	48	10176	100	20986	480, 100, NW_012159984:28893-29952	plot linHum0
289	2013	lipVex1	GCF_000442215.1	SOAPdenovo v. 2.01	292	92	66483	985.5	386576	876, 10, KE557659:158624-160385	plot lipVex1
290	2012	loaLoa1	GCA_000183805.3	Newbler v. 2.1-PreRelease-4/28/2009	376	382	123384	215	94547	604, 20, JH712068v1:803529-804756	plot loaLoa1
291	2005	loxAfr1	tbd	tbd	79	44	11426	206	80801	687, 284, scaffold_10531:71539-73196	plot loxAfr1
292	2008	loxAfr2	tbd	tbd	78	165.5	20735	1078	180887	989, 100, scaffold_3386:17920-19997	plot loxAfr2
293	2009	loxAfr3	GCF_000001905.1	tbd	11	45	1924	398	9784	731, 100, scaffold_211:333226-334787	plot loxAfr3
294	2007	macEug1	tbd	tbd	7319	57	504656	10	562759	146, 1, Scaffold27901:25044-25336	plot macEug1
295	2009	macEug2	GCA_000004035.1	tbd	11689	55	752361	50	1102638	146, 1, GL058785:13153-13445	plot macEug2
296	2013	macFas5	GCF_000364345.1	SOAPdenovo v. 1.0.5, SRPRISM v. 2.4; ARGO v. 0.1	1138	106.5	145024	204.5	1039415	849, 10, chr14:81860376-81862083	plot macFas5
297	2015	macNem1	GCF_000956065.1	AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2; PBJelly2 v. 14.9.9	1828	95	237662	50	834836	982, 25, NW_012016132v1:18826350-18828338	plot macNem1
298	2015	manLeu1	GCF_000951045.1	AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2	6092	95	1723434	50	1354856	1000, 50, NW_012101473v1:89787-91836	plot manLeu1
299	2014	manPen1	GCA_000738955.1	SOAPdenovo v. May 2014	37129	101	5536376	1	13090743	1000, 1, KN006700:349054-351054	plot manPen1
300	2014	manVit1	GCF_000692015.1	SOAPdenovo v. 1.6	25	231	8844	1303	65245	701, 296, KK732740:655429-657126	plot manVit1
302	2012	mayZeb1	GCF_000238955.1	AllPaths v. R37043	1831	95	241336	100	682313	1000, 100, JH720538:3252564-3254663	plot mayZeb1
303	2013	megLyr1	GCA_000465345.1	CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05	33	38	1716	1	185	83, 1, KI087181:1999-2165	plot megLyr1
304	2009	melGal1	tbd	tbd	834	127	136229	100	661041	169, 1, chr3:54352580-54352918	plot melGal1
305	2014	melGal5	GCF_000146605.2	MaSuRCA v. 1.9.2	84	181	17431	100	76065	724, 100, chrZ:7873702-7875249	plot melGal5
308	2008	melInc2	tbd	tbd	3	77	211	201	513	98, 201, MiV1ctg3:286050-286446	plot melInc2
309	2011	melUnd1	GCF_000238935.1	Celera v. 6.1	39	89	5925	41	36796	334, 20, JH556232:114057-114744	plot melUnd1
310	2014	merNub1	GCF_000691845.1	SOAPdenovo v. 1.6	2	154.5	309	361	722	245, 311, KK701714:10568-11368	plot merNub1
311	2013	mesAur1	GCF_000349665.1	allpaths v. R44683	3589	71	248381	100	755166	212, 100, KB708269:3930600-3931123	plot mesAur1
312	2014	mesUni1	GCF_000695765.1	SOAPdenovo v. 1.6	4	347	1434	124.5	451	332, 23, KK817080:7082-7768	plot mesUni1
313	1880	micMur0	tbd	tbd	295	256	90483	780	749299	997, 100, GeneScaffold_4747:166512-168605	plot micMur0
314	2007	micMur1	GCA_000165445.1	tbd	124	124.5	33320	952.5	207469	969, 100, scaffold_5185:107104-109141	plot micMur1
315	2015	micMur2	GCF_000165445.1	AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9	774	90	85250	50	267164	999, 25, KQ057470v1:2292330-2294352	plot micMur2
316	2017	micMur3	GCF_000165445.2	AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9; Lachesis v. shendurelab-LACHESIS-2151de9; BioNano IrysSolve v. 2.1	325	95	73918	50	262987	898, 10, chr2:108635511-108637316	plot micMur3
317	2012	micOch1	GCF_000317375.1	allpaths v. R41985 HAPLOIDIFY=True SPRS_WRITE_SEPS=True	6788	65	483435	100	1507707	993, 100, chr6:54381083-54383168	plot micOch1
318	2011	mm10	tbd	tbd	2	390.5	781	25879.5	51759	477, 1759, chrX_GL456233_random:239940-242652	plot mm10
319	1880	mm5	tbd	tbd	204	48.5	30180	100	76884	921, 100, chr6:132460596-132462537	plot mm5
320	2005	mm6	tbd	tbd	117	48	17647	100	48212	768, 100, chr14:100566071-100567706	plot mm6
321	2005	mm7	tbd	tbd	45	48	5475	100	64491	451, 100, chr15:68974498-68975499	plot mm7
322	2006	mm8	tbd	tbd	6	161	1257	162.5	50878	520, 353, chr14:87009574-87010966	plot mm8
323	2007	mm9	tbd	tbd	2	390.5	781	25879.5	51759	477, 1759, chrX_random:239940-242652	plot mm9
324	2004	monDom1	tbd	tbd	18	53.5	1891	127	11341	696, 100, scaffold_14754:178069-179560	plot monDom1
325	2005	monDom2	tbd	tbd	5	428	2012	100	520	870, 100, scaffold_38:23849795-23851634	plot monDom2
326	2006	monDom4	tbd	tbd	9	183	3070	1000	21732	870, 1, chr1:400420041-400421781	plot monDom4
327	2006	monDom5	tbd	tbd	9	183	3070	1000	21732	870, 1, chr1:424248968-424250708	plot monDom5
328	2013	musDom2	GCF_000371365.1	AllPathsLG v. September 2012	1284	85	165577	1	473996	1000, 1, KB855954:134298-136298	plot musDom2
329	2011	musFur1	GCA_000215625.1	ALLPATHS-LG v. R36167	1009	84	107706	44	286510	1000, 20, GL897138:9717-11736	plot musFur1
330	2013	myoBra1	GCF_000412655.1	SOAP de novo v. 2.04	356	119	85889	1109	766318	1000, 31, KE163605:2655193-2657223	plot myoBra1
331	2012	myoDav1	GCF_000327345.1	SOAPdenovo v. 1.06	303	151	56967	1283	942238	502, 19, KB106370:3092722-3093744	plot myoDav1
332	2006	myoLuc1	tbd	tbd	42	47	6392	1551	125787	388, 100, scaffold_150441:136761-137636	plot myoLuc1
333	2010	myoLuc2	GCF_000147115.1	Arachne v. Dev. Jan 2010	7	39	357	410	3363	75, 119, GL429781:8032929-8033197	plot myoLuc2
334	2014	nanGal1	GCF_000622305.1	SOAPdenovo v. 2.04.4	730	126	149781	902.5	980462	740, 12, KL200152:4088120-4089611	plot nanGal1
335	2015	nanPar1	GCA_000935625.1	SOAPdenovo v. 1.06	1716	194	477991	974	2590489	552, 12, KN907832v1:31307-32422	plot nanPar1
336	2014	nasLar1	GCA_000772465.1	phredPhrap v. 1.080812	614	43	93736	7	126885	117, 1, chr1:6190345-6190579	plot nasLar1
337	2013	necAme1	GCF_000507365.1	Newbler v. MapAsmResearch-04/19/2010-patch-08/17/2010	459	54	28538	100	92887	366, 100, KI657476v1:37386-38217	plot necAme1
338	2007	nemVec1	tbd	tbd	25	378	10288	829	17106	769, 1, scaffold_3968:6459-7997	plot nemVec1
339	2011	neoBri1	GCF_000239395.1	ALLPATHS-LG v. R36800	5040	95	1321574	20	665865	998, 20, JH422308:3325010-3327025	plot neoBri1
340	2017	neoSch1	GCF_002201575.1	RefAligner v. 5122; Supernova v. 1.1	882	47	69252	100	596284	888, 100, NW_018726759v1:1-1876	plot neoSch1
341	2014	nipNip1	GCF_000708225.1	SOAPdenovo v. 1.6	41	154	11937	1090	77358	514, 15, KL411148:2104426-2105468	plot nipNip1
342	2010	nomLeu1	tbd	tbd	859	141	220161	532	1139352	999, 100, GL397299:16863535-16865632	plot nomLeu1
343	2011	nomLeu2	tbd	tbd	859	141	220161	532	1139352	999, 100, GL397299:16863535-16865632	plot nomLeu2
344	2012	nomLeu3	GCA_000146795.3	tbd	861	141	220464	519	1139552	999, 100, chr5:41669854-41671951	plot nomLeu3
345	2014	notCor1	GCF_000735185.1	Celera Assembler v. 7.0	174	91.5	17942	51	21717	407, 1, KL665414:596304-597118	plot notCor1
346	1880	ochPri0	tbd	tbd	569	101	138948	1065	1840608	994, 100, GeneScaffold_4726:276480-278567	plot ochPri0
347	2008	ochPri2	GCA_000164825.1	tbd	313	55	35317	1365	1110261	967, 100, scaffold_3914:61889-63922	plot ochPri2
348	2012	ochPri3	GCF_000292845.1	Allpaths v. R41206	1958	69	148238	100	499781	890, 100, JH802177:1348834-1350713	plot ochPri3
349	2012	octDeg1	GCF_000260255.1	allpaths v. R40507 LITTLE_HELPS_BIG=False	2582	68	231489	100	464548	985, 100, JH651571:12809669-12811738	plot octDeg1
350	2013	odoRosDiv1	GCA_000321225.1	AllPaths v. 41070; Atlas-link v. 1.0; Atlas-gapfill v. 2.2	2581	68	180258	50	263661	970, 50, KB229427:1083192-1085181	plot odoRosDiv1
351	2013	oncVol1	GCA_000499405.1	tbd	10	89.5	2046	1	18211	739, 1, HG738137v1:12037947-12039425	plot oncVol1
352	2014	opiHoa1	GCF_000692075.1	SOAPdenovo v. 1.6	80	170.5	23360	1723.5	216549	855, 28, KK733898:82987-84724	plot opiHoa1
353	2013	orcOrc1	GCF_000331955.2	AllPaths v. 41070; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2	2677	66	181922	50	357696	943, 50, NW_004438742v1:126518-128453	plot orcOrc1
354	2011	oreNil1	tbd	tbd	1903	93	208888	20	734264	969, 20, GL831201:3474999-3476956	plot oreNil1
356	2007	ornAna1	GCF_000002275.2	tbd	793	49	70053	103	148119	718, 10, Contig3645:38619-40064	plot ornAna1
357	2007	ornAna2	GCA_000002275.2	tbd	793	49	70053	103	148119	718, 10, chrUn_DS182721v1:38619-40064	plot ornAna2
358	2012	oryAfe1	GCF_000298275.1	allpaths v. R40776 LITTLE_HELPS_BIG=False	3595	65	293465	100	691489	998, 100, JH863829:9451309-9453404	plot oryAfe1
359	2005	oryCun1	tbd	tbd	122	278.5	44566	462.5	91832	978, 100, scaffold_172390:787-2842	plot oryCun1
360	2009	oryCun2	GCF_000003625.3	tbd	12	44.5	836	446	9055	327, 185, chr13:6520795-6521633	plot oryCun2
361	2006	oryLat1	tbd	tbd	141	144	25310	10	215389	561, 10, chrUn:20300712-20301843	plot oryLat1
362	2005	oryLat2	tbd	tbd	141	144	25310	10	253399	445, 10, ultracontig221:437957-438856	plot oryLat2
364	2011	otoGar3	GCF_000181295.1	ALLPATHS-LG v. R35710	3569	86	332700	39	663694	985, 20, GL873641:2218538-2220527	plot otoGar3
365	2010	oviAri1	GCA_000005525.1	tbd	5934	53	394316	37	1966190	264, 1, chr15:8985870-8986398	plot oviAri1
366	2012	oviAri3	GCF_000298735.1	SOAPdenovo v. 1.03	149	193	51933	215	178445	46, 3, chr3:3466521-3466615	plot oviAri3
367	2015	oviAri4	GCF_000298735.2	SOAPdenovo v. 1.03; PBJelly2 v. 14.9.9	123	285	48608	100	99192	46, 3, chr3:3435119-3435213	plot oviAri4
368	2015	oxyTri2	tbd	tbd	523	37	30028	50	25856	186, 1, chrMACsb310:15510646-15511018	plot oxyTri2
369	2013	panHod1	GCF_000400835.1	SOAPdenovo v. 2.1	321	129	65178	1092	702884	628, 10, KE118776:1218541-1219806	plot panHod1
370	2012	panPan1	GCF_000258655.1	Celera Assembler v. 5.4.3	63	133	11209	20	22114	33, 1, JH650468:842203-842269	plot panPan1
371	2015	panPan2	tbd	tbd	70	160	13388	20	1045522	35, 1, chr4:127787143-127787213	plot panPan2
372	2013	panRed1	GCA_000341325.1	Velvet v. 1.2.07	123	56	6626	10	3069	62, 10, KB454926:42673-42806	plot panRed1
373	2013	panTig1	GCF_000464555.1	SOAPdenovo v. 08-Jul-2011	59	111	12591	700	69429	398, 9, KE721804:6447970-6448774	plot panTig1
374	2003	panTro1	tbd	tbd	5719	388	2244063	100	3504041	998, 100, chr6:137473031-137475126	plot panTro1
375	2006	panTro2	tbd	tbd	692	52	62006	240	238273	717, 10, chr10_random:5205395-5206838	plot panTro2
376	2010	panTro3	tbd	tbd	472	54	44241	238.5	180280	908, 10, chr2B:124438762-124440587	plot panTro3
377	2011	panTro4	GCF_000001515.6	tbd	472	54	44241	238.5	180280	908, 10, chr2B:124438762-124440587	plot panTro4
378	2016	panTro5	GCF_000001515.7	DiscoVar v. 51280; PBJelly v. 14.9.9	2937	199	537385	100	3625772	199, 10, chr12_NW_015974005v1_random:1130-1537	plot panTro5
379	2018	panTro6	GCF_002880755.1	tbd	5	667	3499	100	18496	1000, 100, chr8:127452460-127454559	plot panTro6
380	2012	papAnu2	GCF_000264685.1	CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0	727	138	144060	50	96682	46, 1, chr4:20965571-20965663	plot papAnu2
381	2013	papAnu3	GCF_000264685.2	CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0	727	138	144060	50	96682	46, 1, chr4:20965571-20965663	plot papAnu3
382	2017	papAnu4	GCF_000264685.3	CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0; PBJelly2 v. 14.9.9; Pilon v. 1.18	368	238.5	95783	50	84582	703, 10, chrUn_NW_018824177v1:2651-4066	plot papAnu4
383	2008	papHam1	tbd	tbd	22041	56	1338445	50	2303596	376, 50, scaffold4259:86690-87491	plot papHam1
384	2014	pelCri1	GCF_000687375.1	SOAPdenovo v. 1.6	3	72	517	186	808	386, 173, KK471910:16412-17356	plot pelCri1
385	2011	pelSin1	GCF_000230535.1	SOAPdenovo v. 1.05	126	138	35062	411.5	167243	398, 10, JH212629:287260-288065	plot pelSin1
386	2013	perManBai1	GCF_000500345.1	Newbler v. 2.3 and 2.5; AllPaths v. 41070; ATLAS-gapfill v. 2.2; ATLAS-link v. 1.0	7908	80	846184	50	1552640	1000, 50, KI615759:2266069-2268118	plot perManBai1
387	2007	petMar1	tbd	tbd	542	47	48234	10	42185	746, 10, Contig3178:18125-19626	plot petMar1
388	2010	petMar2	GCA_000148955.1	Arachne v. 3.2	31	86	5681	732	39461	617, 100, GL479790:15647-16980	plot petMar2
389	2017	petMar3	tbd	tbd	40	242.5	11527	100	119063	718, 1, PIZI01000010v1:16691860-16693296	plot petMar3
390	2014	phaCar1	GCF_000708925.1	SOAPdenovo v. 1.6	2	206	412	79	158	261, 100, KL416242:66648-67269	plot phaCar1
391	2014	phaLep1	GCF_000687285.1	SOAPdenovo v. 1.6	14	179	2930	310	4227	343, 85, KK448216:3226-3996	plot phaLep1
392	2014	phoRub1	GCA_000687265.1	SOAPdenovo v. 1.6	4	288.5	1016	195.5	823	373, 83, KK425162:48893-49721	plot phoRub1
393	2013	phyCat1	GCF_000472045.1	AllPaths-LG v. January 2013	684	82.5	86555	100	130377	1000, 1, KI402232:538054-540054	plot phyCat1
394	2014	picPub1	GCF_000699005.1	SOAPdenovo v. 1.6	59	83	12175	970	106482	111, 28, KL217012:74310-74559	plot picPub1
395	2013	poeFor1	GCF_000485575.1	AllPaths-LG v. July 2013	848	75	84492	1	328834	972, 1, KI520524:847-2791	plot poeFor1
396	2014	poeRet1	tbd	tbd	1124	87	157426	1	421252	988, 1, chrLG12:26078504-26080480	plot poeRet1
397	1880	ponAbe1	tbd	tbd	1528	40	90824	133.5	275853	662, 10, Contig208:1185633-1186966	plot ponAbe1
398	2007	ponAbe2	tbd	tbd	2239	54	444541	100	829820	769, 1, chr11:46659515-46661053	plot ponAbe2
400	2014	priExs1	tbd	tbd	49	121	12100	1773	95166	181, 38, scaffold470:42605-43004	plot priExs1
401	2007	priPac1	tbd	tbd	121	49	10688	209	31254	90, 1, chrUn:114913780-114913960	plot priPac1
403	2014	priPac3	tbd	tbd	168	49.5	13153	274.5	50322	90, 1, Ppa_Contig2432:805-985	plot priPac3
404	2008	proCap1	GCA_000152225.1	Arachne v. before 2009	116	38	5205	534.5	65619	53, 100, scaffold_8867:32393-32598	plot proCap1
405	2015	proCoq1	GCF_000956105.1	AllPathsLG v. R43839; Atlas Link v. 1.0; Atlas Gapfill v. 2.2	1491	92	191552	50	427249	970, 50, NW_012149019v1:36737-38726	plot proCoq1
406	2013	pseHum1	GCF_000331425.1	SOAPdenovo v. 1.5	775	142	173055	10	547111	1000, 10, KB221227:5459003-5461012	plot pseHum1
407	2012	pteAle1	GCA_000325575.1	SOAPdenovo v. 1.06	97	127	19728	1023	161616	421, 16, KB031157:14150143-14151000	plot pteAle1
408	2014	pteGut1	GCF_000699245.1	SOAPdenovo v. 1.6	1	282	282	720	720	282, 720, KL237369:530-1813	plot pteGut1
409	2013	ptePar1	GCA_000465405.1	CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05	3	31	102	1	3	40, 1, KE827285:1815-1895	plot ptePar1
410	2008	pteVam1	GCA_000151845.1	tbd	68	43.5	9173	301.5	27212	971, 100, scaffold_4327:120126-122167	plot pteVam1
411	2011	punNye1	GCF_000239375.1	ALLPATHS-LG v. R37016	1574	95	242736	20	332782	992, 20, JH419321:67178-69181	plot punNye1
412	2014	pygAde1	GCA_000699105.1	SOAPdenovo v. 1.6	42	113	7740	1160.5	93198	78, 17, KL224983:2418932-2419104	plot pygAde1
413	2013	pytBiv1	GCF_000186305.1	Soap deNovo v. March 2012	21222	101	2315791	99	2845128	649, 10, KE957835:3697-5004	plot pytBiv1
418	2005	rheMac1	tbd	tbd	2816	39	116369	50	214725	205, 50, SCAFFOLD120616:17732-18191	plot rheMac1
419	2010	rheMac3	GCA_000230795.1	SOAPdenovo v. 1.0	288	192.5	71777	1140.5	887215	949, 27, chr15:33329332-33331256	plot rheMac3
420	2015	rheMac8	GCF_000772875.2	MaSuRCA v. 1.8.3; PBJelly2 v. 14.9.9	80	99.5	20122	917	437685	823, 20, chr7:1436259-1437924	plot rheMac8
421	2016	rhiBie1	GCF_001698545.1	Newbler v. 71; Anytag v. 70; GOBOND v. 69; GapCloser v. 1.12	4262	228	1007049	1	2148972	965, 1, NW_016817388v1:689035-690965	plot rhiBie1
422	2013	rhiFer1	GCA_000465495.1	CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05	2	42.5	85	1	2	45, 1, KI143993:8550-8640	plot rhiFer1
423	2014	rhiRox1	GCF_000769185.1	SOAPdenovo v. 2013.04	187	158	50999	529	184770	584, 11, KN296100v1:378785-379963	plot rhiRox1
424	1880	ricCom1	GCF_000151685.1	tbd	41	332	13808	738	38675	787, 3, EQ973819:99412-100988	plot ricCom1
425	2003	rn3	tbd	tbd	574	143	146802	50	425043	72, 1, chr4:1247786-1247930	plot rn3
426	2004	rn4	tbd	tbd	567	141	142452	50	424693	72, 1, chr4:1247786-1247930	plot rn4
427	2012	rn5	tbd	tbd	64	516	32231	50	28921	712, 1, chr3:45275318-45276742	plot rn5
428	2014	rn6	GCF_000001895.5	Atlas Assembly suite v. 2.0; CLCbio v. 1.0; Velvet v. 1.0; PBjelly v. 2.0	719	290	280406	50	1258566	712, 1, chr3:40184108-40185532	plot rn6
433	2011	saiBol1	GCA_000235385.1	AllPaths v. R37830	1541	77	139356	100	303093	1000, 100, JH378136:528784-530883	plot saiBol1
435	2011	sarHar1	GCF_000189315.1	Phusion2 v. 1.0	17494	220	2993318	158	6574378	958, 10, chr1_GL834475_random:882665-884590	plot sarHar1
436	2013	sebNig1	GCA_000475235.1	tbd	168	55.5	11782	54.5	11235	82, 2, KI499294:4621-4786	plot sebNig1
437	2013	sebRub1	GCA_000475215.1	SOAPdenovo v. 1.05	119	55	9711	51	8253	142, 1, KI444651:3586-3870	plot sebRub1
438	2014	serCan1	GCF_000534875.1	tbd	213	97	36640	20	33876	971, 1, HG009242:4536330-4538272	plot serCan1
439	2006	sorAra1	tbd	tbd	229	330	79670	100	75086	895, 100, scaffold_247593:25660-27549	plot sorAra1
440	2008	sorAra2	GCF_000181275.1	Allpaths v. R41070	3389	75	359891	100	822102	992, 100, JH798160:15867029-15869112	plot sorAra2
441	2008	speTri1	tbd	tbd	99	46	12167	879	197520	835, 100, scaffold_1259:158788-160557	plot speTri1
442	2011	speTri2	GCF_000236235.1	ALLPATHS v. R37591	2964	95	353556	100	565083	1000, 100, JH393486:3045059-3047158	plot speTri2
444	2014	stePar1	GCF_000690725.1	ALLPATHS-LG v. August 2013	554	65	47063	1	120402	952, 1, KK580894:321554-323458	plot stePar1
445	1880	strCam0	tbd	tbd	20	243	7267	836.5	40260	184, 13, superscaffold45:7169362-7169742	plot strCam0
446	2014	strCam1	GCF_000698965.1	SOAPdenovo v. 1.6	19	246	7125	759	39346	184, 13, KL206666:4120006-4120386	plot strCam1
447	2005	strPur1	tbd	tbd	1291	153	303896	50	238579	89, 1, Scaffold16400:576-754	plot strPur1
448	2006	strPur2	tbd	tbd	367	55	25281	50	79238	35, 1, Scaffold12735:108654-108724	plot strPur2
449	2009	strPur3	tbd	tbd	989	56	64991	96	187408	35, 1, Scaffold740:110486-110556	plot strPur3
450	2011	strPur4	GCF_000002235.3	Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement	1612	100	326953	50	206009	425, 3, Scaffold112:361603-362455	plot strPur4
452	2014	strRat2	GCA_001040885.1	tbd	2	54.5	109	6	12	67, 1, chrUn_LN609483v1:243-377	plot strRat2
454	2009	susScr1	tbd	tbd	371	43	34151	100	66500	986, 100, chr2:139016697-139018768	plot susScr1
455	2017	susScr11	GCF_000003025.6	Falcon v. OCT-2015	2	104.5	209	100	200	110, 100, chrY:6779476-6779795	plot susScr11
456	2009	susScr2	tbd	tbd	371	43	34151	100	66500	986, 100, chr2:139016697-139018768	plot susScr2
457	1880	taeGut0	tbd	tbd	212	45	20495	442	116920	624, 10, Contig233:50949-52206	plot taeGut0
458	2008	taeGut1	tbd	tbd	223	45	22373	100	22300	689, 100, chr21_random:54357-55834	plot taeGut1
459	2013	taeGut2	GCF_000151805.1	PCAP v. 2008	219	44	21273	100	21900	624, 100, chr27:56676-58023	plot taeGut2
461	2013	takFla1	GCA_000400755.1	HAPs v. 0.2.2	365	241	91817	788	407496	503, 1, KE121297:329-1335	plot takFla1
462	2013	tarIhg38	tbd	tbd	12	78	974	440	56689	125, 20, chrUn_KI270442v1:175618-175887	plot tarIhg38
463	2008	tarSyr1	tbd	tbd	331	70	45530	191	102767	892, 100, scaffold_111889:3660-5543	plot tarSyr1
464	2013	tarSyr2	GCF_000164805.1	Celera v. DEC-2012	189	56	17645	20	9572	1000, 20, KE939253v1:939796-941815	plot tarSyr2
465	2014	tauEry1	GCF_000709365.1	SOAPdenovo v. 1.6	1	50	50	394	394	50, 394, KL466072:20829-21322	plot tauEry1
466	2004	tetNig1	tbd	tbd	64	272.5	21868	1000	53904	336, 59, chr5:807217-807947	plot tetNig1
467	2007	tetNig2	tbd	tbd	70	298	25569	500	32404	336, 59, chr5:799217-799947	plot tetNig2
468	2015	thaSir1	GCF_001077635.1	ALLPATHS-LG v. May 2015	3234	95	407625	666	2420576	981, 1, NW_013657934v1:351094-353056	plot thaSir1
469	2014	tinGut1	GCF_000705375.1	SOAPdenovo v. 1.6	18	96	3855	1086	21982	519, 68, KL400865:236113-237218	plot tinGut1
470	2014	tinGut2	GCF_000705375.1	SOAPdenovo v. 1.6	18	96	3855	1086	21982	519, 68, KL895544:236113-237218	plot tinGut2
471	2005	triCas1	tbd	tbd	75	100	8201	50	6900	214, 50, Contig5855_Contig1469:226794-227271	plot triCas1
472	2005	triCas2	tbd	tbd	63	62	5442	50	313244	412, 50, chrUn_46:283716-284589	plot triCas2
473	2011	triMan1	GCF_000243295.1	AllPaths v. R38542	5748	75	527972	100	726640	1000, 100, JH594622:8537918-8540017	plot triMan1
474	2011	triSpi1	GCF_000181795.1	PCAP v. January 12, 2007	3	55	806	10	230	705, 10, GL622790v1:172202-173621	plot triSpi1
475	2014	triSui1	GCA_000701005.1	SOAPdenovo v. 2	37	138	7959	1449	82883	120, 68, KL363219v1:83933-84240	plot triSui1
477	2013	tupChi1	GCF_000334495.1	SOAPdenovo v. 1.05	914	220.5	290632	987.5	1823897	861, 16, KB320907:3306581-3308318	plot tupChi1
478	2008	turTru1	tbd	tbd	112	41.5	15556	388	52461	993, 100, scaffold_108458:6669-8754	plot turTru1
479	2011	turTru2	GCF_000151865.2	Atlas, Atlas-Link, Atlas-GapFill v. June 2011	5612	70	466776	188.5	1979352	44, 1, JH496197:2095-2183	plot turTru2
480	2014	tytAlb1	GCF_000687205.1	SOAPdenovo v. 1.6	2	170	340	326	652	289, 220, KK379918:2163-2960	plot tytAlb1
481	2014	ursMar1	GCF_000687225.1	SOAPdenovo v. 1.05	205	41	12130	3384	708704	711, 49, KK498595:3401141-3402611	plot ursMar1
482	2007	venter1	tbd	tbd	64	411.5	26995	100	64592	862, 20, chr2:102870978-102872721	plot venter1
483	2008	vicPac1	tbd	tbd	221	251	71912	276	310711	993, 100, scaffold_812:411693-413778	plot vicPac1
484	2013	vicPac2	GCF_000164845.1	Newbler v. May-2012	1245	69	115488	369	430947	685, 20, KB632527:971889-973278	plot vicPac2
485	1880	vicVic1	tbd	tbd	218	252.5	71401	263	309237	993, 100, scaffold_812:411693-413778	plot vicVic1
486	2016	xenLae2	GCF_001663975.1	Meraculous v. May-2013	2660	43	112843	265	1906995	50, 10, chr6S:105116072-105116181	plot xenLae2
487	2004	xenTro1	tbd	tbd	140	177.5	37717	889.5	437093	94, 1, scaffold_26179:153-341	plot xenTro1
488	2005	xenTro2	tbd	tbd	116	229.5	33928	806.5	320973	83, 1, scaffold_13788:6263-6429	plot xenTro2
489	2009	xenTro3	tbd	tbd	116	229.5	33928	806.5	320973	83, 1, GL185958:6263-6429	plot xenTro3
490	2012	xenTro7	GCF_000004195.2	ARACHNE v. 20071016_modified	98	82.5	16149	201	69741	775, 100, KB022861:7377-9026	plot xenTro7
491	2016	xenTro9	GCF_000004195.3	Meraculous v. May-2013	172	105.5	27368	100	99243	775, 100, chrUn_NW_016684502v1:7377-9026	plot xenTro9
492	2012	xipMac1	GCF_000241075.1	PCAP v. 3/30/09; Newbler v. MapAsmResearch-02/17/2010	548	50	32896	131	334271	30, 1, JH556915:15756-15816	plot xipMac1
494	2013	zonAlb1	GCF_000385455.1	Allpaths-LG v. Feb-2013	538	79	50834	1	134738	990, 1, KB913055:7474487-7476467	plot zonAlb1

assemblies with zero duplicate gap sequences

count	year	dbName	ncbiAsmId	number of gaps	assembly method
001	2012	aciBauTYTH_1	GCF_000302575.1	4	tbd
002	2006	afrOth13	tbd	220	tbd
003	2014	apaVit1	GCF_000703405.1	50921	SOAPdenovo v. 1.6
004	2018	astCal1	tbd	395	tbd
005	2006	borEut13	tbd	0	tbd
006	2014	bunEbo1	GCF_000889155.1	0	tbd
007	2010	caeJap3	tbd	0	tbd
008	2003	canFamPoodle1	GCA_000181415.1	0	tbd
009	2005	canHg12	tbd	0	tbd
010	2010	ce10	tbd	0	tbd
011	2013	ce11	GCF_000002985.6	0	tbd
012	2004	ce2	tbd	5	tbd
013	2005	ce3	tbd	0	tbd
014	2007	ce4	tbd	0	tbd
015	2007	ce5	tbd	0	tbd
016	2008	ce6	tbd	0	tbd
017	2009	ce7	tbd	0	tbd
018	2009	ce8	tbd	0	tbd
019	2010	ce9	tbd	0	tbd
020	2004	droMoj1	tbd	0	tbd
021	2014	eboVir1	tbd	2	tbd
022	2014	eboVir3	tbd	0	tbd
023	2006	euaGli13	tbd	19510	tbd
024	2006	eutHer13	tbd	304	tbd
025	2017	felCat9	GCF_000181335.3	418	WTDBG v. 1.2, Chromonomer v. 1.0.7
026	2018	galGal6	GCF_000002315.5	943	FALCON-integrate v. 1.7.5
027	1880	gasAsc0	GCA_000180675.1	0	tbd
028	2006	gliRes13	tbd	39623	tbd
029	2016	gorGor5	tbd	0	tbd
030	1993	hbv1	GCF_000861825.2	0	tbd
031	2006	homIni14	tbd	0	tbd
032	1880	homNea0	tbd	872	tbd
033	2002	hpv1	GCF_000862685.1	0	tbd
034	2006	lauRas13	tbd	31794	tbd
035	2014	marVir1	tbd	0	tbd
036	2008	melHap1	GCA_000172435.1	0	tbd
037	2008	melInc1	GCA_000180415.1	0	tbd
038	2016	oreNil3	GCF_001858045.1	424	Canu v. 1.0; Chromonomer v. 1.05
039	2006	otoGar1	tbd	0	tbd
040	2018	ponAbe3	GCF_002880775.1	553	Falcon v. (git hash: 91e700c4) Nov 2015; BioNano Access Hybrid Scaffolds
041	2008	priPac2	GCA_000180635.1	59	tbd
042	2012	repBase0	tbd	2137	tbd
043	2012	repBase1	tbd	3623	tbd
044	1880	repBase2	tbd	3237	tbd
045	2014	resEbo1	GCF_000854085.1	0	tbd
046	2016	rouAeg1	GCF_001466805.2	638	SparseAssembler v. OCTOBER-2015; DBG2OLC v. OCTOBER-2015; LINKS v. 1.5.1; L_RNA_Scaffolder v. OCTOBER-2015; SSPACE v. 3.0
047	2003	sacCer1	tbd	0	tbd
048	2008	sacCer2	tbd	0	tbd
049	2011	sacCer3	GCF_000146045.2	0	tbd
050	1880	salMan0	tbd	0	tbd
051	2006	staAur1	GCF_000013425.1	1	tbd
052	2011	strRat1	tbd	3207	tbd
053	2014	sudEbo1	GCF_000855585.1	0	tbd
054	2014	taiEbo1	GCF_000888475.1	0	tbd
055	2006	tupBel1	tbd	0	tbd
056	2014	zaiEbo1	GCF_000848505.1	0	tbd

GapOverlap: Difference between revisions

Latest revision as of 19:01, 8 March 2019

Contents

methods

table features

gapOverlap table statistics

assemblies with zero duplicate gap sequences

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@@ Line 49: / Line 49: @@
 ! item
 total
-| &nbsp;
 ! gap
 median
@@ Line 61: / Line 60: @@
 | 001
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CBA_J CBA_J]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CBA_J CBA_J]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624475.1/ GCA_001624475.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 67: / Line 66: @@
 | style='text-align:right'| 279.5
 | style='text-align:right'| 7933814
-| &nbsp;
 | style='text-align:right'| 26
 | style='text-align:right'| 26736971
-| 999,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CBA_J&position=chr16:100093490-100095488 chr16:100093490-100095488]
+| 999,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CBA_J&position=chr16:100093490-100095488 chr16:100093490-100095488]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624475.1_CBA_J_v1 plot GCA_001624475.1_CBA_J_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624475.1_CBA_J_v1 plot GCA_001624475.1_CBA_J_v1]
 |-
 | 002
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PAHARI_EIJ PAHARI_EIJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PAHARI_EIJ PAHARI_EIJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_900095145.1/ GCA_900095145.1]
 | tbd
@@ Line 81: / Line 79: @@
 | style='text-align:right'| 69
 | style='text-align:right'| 479534
-| &nbsp;
 | style='text-align:right'| 1
 | style='text-align:right'| 675789
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PAHARI_EIJ&position=chr7:107557946-107559946 chr7:107557946-107559946]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PAHARI_EIJ&position=chr7:107557946-107559946 chr7:107557946-107559946]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_900095145.1_PAHARI_EIJ_v1 plot GCA_900095145.1_PAHARI_EIJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_900095145.1_PAHARI_EIJ_v1 plot GCA_900095145.1_PAHARI_EIJ_v1]
 |-
 | 003
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PWK_PhJ PWK_PhJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PWK_PhJ PWK_PhJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624775.1/ GCA_001624775.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 95: / Line 92: @@
 | style='text-align:right'| 65
 | style='text-align:right'| 16823451
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 10585326
-| 1000,	11,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PWK_PhJ&position=chrX:47500642-47502652 chrX:47500642-47502652]
+| 1000,	11,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=PWK_PhJ&position=chrX:47500642-47502652 chrX:47500642-47502652]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624775.1_PWK_PhJ_v1 plot GCA_001624775.1_PWK_PhJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624775.1_PWK_PhJ_v1 plot GCA_001624775.1_PWK_PhJ_v1]
 |-
 | 004
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=SPRET_EiJ SPRET_EiJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=SPRET_EiJ SPRET_EiJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624865.1/ GCA_001624865.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail genomics v. August-2015; Ragout v. 2.0b
@@ Line 109: / Line 105: @@
 | style='text-align:right'| 516
 | style='text-align:right'| 8157541
-| &nbsp;
 | style='text-align:right'| 100
 | style='text-align:right'| 12022683
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=SPRET_EiJ&position=chr10:66049175-66051175 chr10:66049175-66051175]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=SPRET_EiJ&position=chr10:66049175-66051175 chr10:66049175-66051175]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624865.1_SPRET_EiJ_v1 plot GCA_001624865.1_SPRET_EiJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624865.1_SPRET_EiJ_v1 plot GCA_001624865.1_SPRET_EiJ_v1]
 |-
 | 005
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NZO_HlLtJ NZO_HlLtJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NZO_HlLtJ NZO_HlLtJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624745.1/ GCA_001624745.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 123: / Line 118: @@
 | style='text-align:right'| 448
 | style='text-align:right'| 8647582
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 14665906
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NZO_HlLtJ&position=chr10:29328015-29330015 chr10:29328015-29330015]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NZO_HlLtJ&position=chr10:29328015-29330015 chr10:29328015-29330015]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624745.1_NZO_HlLtJ_v1 plot GCA_001624745.1_NZO_HlLtJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624745.1_NZO_HlLtJ_v1 plot GCA_001624745.1_NZO_HlLtJ_v1]
 |-
 | 006
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=129S1_SvImJ 129S1_SvImJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=129S1_SvImJ 129S1_SvImJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624185.1/ GCA_001624185.1]
 | SGA v. 0.9.19; Ragout v. 2.0b
@@ Line 137: / Line 131: @@
 | style='text-align:right'| 400
 | style='text-align:right'| 7813478
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 15456883
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=129S1_SvImJ&position=chr15:34994444-34996444 chr15:34994444-34996444]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=129S1_SvImJ&position=chr15:34994444-34996444 chr15:34994444-34996444]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624185.1_129S1_SvImJ_v1 plot GCA_001624185.1_129S1_SvImJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624185.1_129S1_SvImJ_v1 plot GCA_001624185.1_129S1_SvImJ_v1]
 |-
 | 007
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C57BL_6NJ C57BL_6NJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C57BL_6NJ C57BL_6NJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001632555.1/ GCA_001632555.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 151: / Line 144: @@
 | style='text-align:right'| 97
 | style='text-align:right'| 6239791
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 14404336
-| 992,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C57BL_6NJ&position=chr10:109927459-109929443 chr10:109927459-109929443]
+| 992,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C57BL_6NJ&position=chr10:109927459-109929443 chr10:109927459-109929443]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632555.1_C57BL_6NJ_v1 plot GCA_001632555.1_C57BL_6NJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632555.1_C57BL_6NJ_v1 plot GCA_001632555.1_C57BL_6NJ_v1]
 |-
 | 008
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=AKR_J AKR_J]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=AKR_J AKR_J]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624295.1/ GCA_001624295.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 165: / Line 157: @@
 | style='text-align:right'| 335
 | style='text-align:right'| 6717178
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 14468858
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=AKR_J&position=chr16:53464467-53466467 chr16:53464467-53466467]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=AKR_J&position=chr16:53464467-53466467 chr16:53464467-53466467]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624295.1_AKR_J_v1 plot GCA_001624295.1_AKR_J_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624295.1_AKR_J_v1 plot GCA_001624295.1_AKR_J_v1]
 |-
 | 009
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C3H_HeJ C3H_HeJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C3H_HeJ C3H_HeJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001632575.1/ GCA_001632575.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 179: / Line 170: @@
 | style='text-align:right'| 307
 | style='text-align:right'| 6287513
-| &nbsp;
 | style='text-align:right'| 26
 | style='text-align:right'| 12931709
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C3H_HeJ&position=chr1:52782023-52784023 chr1:52782023-52784023]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=C3H_HeJ&position=chr1:52782023-52784023 chr1:52782023-52784023]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632575.1_C3H_HeJ_v1 plot GCA_001632575.1_C3H_HeJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632575.1_C3H_HeJ_v1 plot GCA_001632575.1_C3H_HeJ_v1]
 |-
 | 010
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=FVB_NJ FVB_NJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=FVB_NJ FVB_NJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624535.1/ GCA_001624535.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 193: / Line 183: @@
 | style='text-align:right'| 355
 | style='text-align:right'| 4902432
-| &nbsp;
 | style='text-align:right'| 11
 | style='text-align:right'| 8504942
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=FVB_NJ&position=chr17:22790916-22792916 chr17:22790916-22792916]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=FVB_NJ&position=chr17:22790916-22792916 chr17:22790916-22792916]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624535.1_FVB_NJ_v1 plot GCA_001624535.1_FVB_NJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624535.1_FVB_NJ_v1 plot GCA_001624535.1_FVB_NJ_v1]
 |-
 | 011
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=WSB_EiJ WSB_EiJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=WSB_EiJ WSB_EiJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624835.1/ GCA_001624835.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 207: / Line 196: @@
 | style='text-align:right'| 236
 | style='text-align:right'| 3524308
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 10785288
-| 994,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=WSB_EiJ&position=chrX:58921651-58923639 chrX:58921651-58923639]
+| 994,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=WSB_EiJ&position=chrX:58921651-58923639 chrX:58921651-58923639]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624835.1_WSB_EiJ_v1 plot GCA_001624835.1_WSB_EiJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624835.1_WSB_EiJ_v1 plot GCA_001624835.1_WSB_EiJ_v1]
 |-
 | 012
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=A_J A_J]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=A_J A_J]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624215.1/ GCA_001624215.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 221: / Line 209: @@
 | style='text-align:right'| 80
 | style='text-align:right'| 6428892
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 14025482
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=A_J&position=chr17:63064911-63066911 chr17:63064911-63066911]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=A_J&position=chr17:63064911-63066911 chr17:63064911-63066911]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624215.1_A_J_v1 plot GCA_001624215.1_A_J_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624215.1_A_J_v1 plot GCA_001624215.1_A_J_v1]
 |-
 | 013
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAROLI_EIJ CAROLI_EIJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAROLI_EIJ CAROLI_EIJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_900094665.1/ GCA_900094665.1]
 | tbd
@@ Line 235: / Line 222: @@
 | style='text-align:right'| 70
 | style='text-align:right'| 484857
-| &nbsp;
 | style='text-align:right'| 1
 | style='text-align:right'| 599072
-| 945,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAROLI_EIJ&position=chr1:145228793-145230683 chr1:145228793-145230683]
+| 945,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAROLI_EIJ&position=chr1:145228793-145230683 chr1:145228793-145230683]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_900094665.1_CAROLI_EIJ_v1 plot GCA_900094665.1_CAROLI_EIJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_900094665.1_CAROLI_EIJ_v1 plot GCA_900094665.1_CAROLI_EIJ_v1]
 |-
 | 014
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=LP_J LP_J]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=LP_J LP_J]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001632615.1/ GCA_001632615.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 249: / Line 235: @@
 | style='text-align:right'| 98
 | style='text-align:right'| 5185817
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 13674278
-| 997,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=LP_J&position=chr12:42758762-42760756 chr12:42758762-42760756]
+| 997,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=LP_J&position=chr12:42758762-42760756 chr12:42758762-42760756]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632615.1_LP_J_v1 plot GCA_001632615.1_LP_J_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632615.1_LP_J_v1 plot GCA_001632615.1_LP_J_v1]
 |-
 | 015
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=BALB_cJ BALB_cJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=BALB_cJ BALB_cJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001632525.1/ GCA_001632525.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 263: / Line 248: @@
 | style='text-align:right'| 363
 | style='text-align:right'| 5543975
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 10053337
-| 999,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=BALB_cJ&position=chr4:59636957-59638955 chr4:59636957-59638955]
+| 999,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=BALB_cJ&position=chr4:59636957-59638955 chr4:59636957-59638955]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632525.1_BALB_cJ_v1 plot GCA_001632525.1_BALB_cJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001632525.1_BALB_cJ_v1 plot GCA_001632525.1_BALB_cJ_v1]
 |-
 | 016
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=DBA_2J DBA_2J]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=DBA_2J DBA_2J]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624505.1/ GCA_001624505.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 277: / Line 261: @@
 | style='text-align:right'| 98
 | style='text-align:right'| 3606947
-| &nbsp;
 | style='text-align:right'| 25
 | style='text-align:right'| 7251641
-| 999,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=DBA_2J&position=chr10:47277903-47279901 chr10:47277903-47279901]
+| 999,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=DBA_2J&position=chr10:47277903-47279901 chr10:47277903-47279901]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624505.1_DBA_2J_v1 plot GCA_001624505.1_DBA_2J_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624505.1_DBA_2J_v1 plot GCA_001624505.1_DBA_2J_v1]
 |-
 | 017
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NOD_ShiLtJ NOD_ShiLtJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NOD_ShiLtJ NOD_ShiLtJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624675.1/ GCA_001624675.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b
@@ Line 291: / Line 274: @@
 | style='text-align:right'| 172
 | style='text-align:right'| 10515906
-| &nbsp;
 | style='text-align:right'| 26
 | style='text-align:right'| 25076950
-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NOD_ShiLtJ&position=chr15:69777938-69779938 chr15:69777938-69779938]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=NOD_ShiLtJ&position=chr15:69777938-69779938 chr15:69777938-69779938]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624675.1_NOD_ShiLtJ_v1 plot GCA_001624675.1_NOD_ShiLtJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624675.1_NOD_ShiLtJ_v1 plot GCA_001624675.1_NOD_ShiLtJ_v1]
 |-
 | 018
 | 2016
-| style='text-align:center;'| [http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAST_EiJ CAST_EiJ]
+| style='text-align:center;'| [http://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAST_EiJ CAST_EiJ]
 | style='text-align:center;'| [https://www.ncbi.nlm.nih.gov/assembly/GCA_001624445.1/ GCA_001624445.1]
 | SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail Genomics v. August-2015; Ragout v. 2.0b
@@ Line 305: / Line 287: @@
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-| 1000,	1,	[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.cse.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAST_EiJ&position=chr12:100100159-100102159 chr12:100100159-100102159]
+| 1000,	1,	[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-test.gi.ucsc.edu/hubs/mouseStrains/hub.txt&genome=CAST_EiJ&position=chr12:100100159-100102159 chr12:100100159-100102159]
-| [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624445.1_CAST_EiJ_v1 plot GCA_001624445.1_CAST_EiJ_v1]
+| [http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/gapOverlap?db=GCA_001624445.1_CAST_EiJ_v1 plot GCA_001624445.1_CAST_EiJ_v1]
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-| &nbsp;
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-| &nbsp;
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-| &nbsp;
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-| &nbsp;
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-| &nbsp;
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@@ Line 6,087: / Line 5,656: @@
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@@ Line 6,101: / Line 5,669: @@
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-| &nbsp;
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@@ Line 6,115: / Line 5,682: @@
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-| &nbsp;
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 | style='text-align:right'| 229.5
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-| &nbsp;
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@@ Line 6,143: / Line 5,708: @@
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-| &nbsp;
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 | style='text-align:right'| 69741
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-| &nbsp;
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@@ Line 6,185: / Line 5,747: @@
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-| &nbsp;
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 | style='text-align:right'| 134738