GapOverlap
From genomewiki
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 | 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 | |
| 002 | 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 | |
| 003 | 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 | |
| 004 | 2016 | CAROLI_EIJ | GCA_900094665.1 | tbd | 6469 | 70 | 484857 | 1 | 599072 | 945, 1, chr1:145228793-145230683 | plot GCA_900094665.1_CAROLI_EIJ_v1 | |
| 005 | 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 | |
| 006 | 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 | |
| 007 | 2016 | PAHARI_EIJ | GCA_900095145.1 | tbd | 6365 | 69 | 479534 | 1 | 675789 | 1000, 1, chr7:107557946-107559946 | plot GCA_900095145.1_PAHARI_EIJ_v1 | |
| 008 | 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 | |
| 009 | 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 | |
| 010 | 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 | |
| 011 | 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 | |
| 012 | 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 | |
| 013 | 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 | |
| 014 | 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 | |
| 015 | 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 | |
| 016 | 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 | |
| 017 | 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 | |
| 018 | 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 | |
| 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 | 2014 | acaChl1 | GCF_000695815.1 | SOAPdenovo v. 1.6 | 5 | 170 | 1250 | 188 | 2340 | 722, 188, KK833582:5976-7607 | plot acaChl1 | |
| 023 | 2009 | ailMel1 | GCF_000004335.2 | tbd | 48 | 104 | 10594 | 1193 | 82504 | 75, 1, GL192694.1:348745-348895 | plot ailMel1 | |
| 024 | 2012 | allMis1 | GCF_000281125.1 | Allpaths v. R41313; manual scaffolding | 1151 | 83 | 273934 | 1 | 74939 | 999, 1, JH739280:136433-138431 | plot allMis1 | |
| 025 | 2013 | allSin1 | GCF_000455745.1 | SOAPdenovo v. 1.05 | 95 | 125 | 26114 | 2265 | 261774 | 69, 10, KE696011:2095494-2095641 | plot allSin1 | |
| 026 | 2013 | amaVit1 | GCA_000332375.1 | Ray software v. 3 | 10099 | 81 | 1392334 | 172 | 2756641 | 492, 13, KB238901:2710-3706 | plot amaVit1 | |
| 027 | 2013 | anaPla1 | GCF_000355885.1 | SOAPdenovo Release v. 1.03 | 31 | 251 | 10663 | 1660 | 94318 | 99, 1, KB742632:907264-907462 | plot anaPla1 | |
| 028 | 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 | |
| 029 | 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 | |
| 030 | 2007 | anoCar1 | tbd | tbd | 20 | 383.5 | 8167 | 537.5 | 23338 | 965, 100, scaffold_84:3853690-3855719 | plot anoCar1 | |
| 031 | 2010 | anoCar2 | GCF_000090745.1 | Arachne v. 3.0.0 | 25 | 240 | 6694 | 258 | 26105 | 318, 100, chr4:54548520-54549255 | plot anoCar2 | |
| 032 | 2003 | anoGam1 | tbd | tbd | 7 | 528 | 3139 | 1000 | 21041 | 1000, 384, chr2L:5019927-5022310 | plot anoGam1 | |
| 033 | 2013 | apaSpi1 | GCA_000385615.1 | SOAPdenovo v. 1.0.5 | 607 | 61 | 34340 | 100 | 56961 | 86, 10, KB929338:2579176-2579357 | plot apaSpi1 | |
| 035 | 2004 | apiMel1 | tbd | tbd | 216 | 50 | 12150 | 10 | 24454 | 64, 1, Group14.17:517485-517613 | plot apiMel1 | |
| 036 | 2005 | apiMel2 | tbd | tbd | 133 | 50 | 7371 | 50 | 19757 | 168, 50, Group4:4855105-4855490 | plot apiMel2 | |
| 037 | 2005 | apiMel3 | tbd | tbd | 199 | 62 | 16045 | 50 | 27354 | 198, 50, Group15:1672512-1672957 | plot apiMel3 | |
| 038 | 2010 | apiMel4 | GCF_000002195.4 | Atlas assembly system v. before 2011 | 226 | 52.5 | 13378 | 50 | 24561 | 167, 50, Group14:1674117-1674500 | plot apiMel4 | |
| 039 | 2008 | aplCal1 | tbd | tbd | 25 | 77 | 3383 | 100 | 16863 | 390, 100, scaffold_1802:24095-24974 | plot aplCal1 | |
| 040 | 2014 | aptFor1 | GCF_000699145.1 | SOAPdenovo v. 1.6 | 109 | 147 | 26798 | 1575 | 323838 | 779, 98, KL225582:135043-136698 | plot aptFor1 | |
| 041 | 2015 | aptMan1 | GCF_001039765.1 | tbd | 15742 | 124 | 4653010 | 1 | 3331011 | 1000, 1, NW_013987125v1:2508272-2510272 | plot aptMan1 | |
| 042 | 2014 | aquChr1 | GCA_000696035.1 | ABySS v. 1.3.6 | 4592 | 43 | 201248 | 65 | 16118238 | 65, 1, KK850461:8872-9002 | plot aquChr1 | |
| 043 | 2014 | aquChr2 | GCA_000766835.1 | AllPaths-LG v. August 2013 | 326 | 82.5 | 31349 | 1 | 143600 | 1000, 1, KN265664v1:16826772-16828772 | plot aquChr2 | |
| 044 | 2013 | araMac1 | GCA_000400695.1 | CLC Genomics Workbench v. 4.9 | 120 | 48.5 | 7929 | 33 | 27135 | 241, 2, KE047968:4314-4797 | plot araMac1 | |
| 045 | 1880 | araTha1 | GCF_000001735.3 | tbd | 1 | 289 | 289 | 60 | 60 | 289, 60, chr3:13855281-13855918 | plot araTha1 | |
| 046 | 2012 | ascSuu1 | GCA_000298755.1 | SOAPdenovo v. 1.04 | 9 | 404 | 3688 | 555 | 6481 | 1000, 247, JH879107v1:69728-71974 | plot ascSuu1 | |
| 047 | 2013 | astMex1 | GCF_000372685.1 | AllPathsLG v. Jan-2013 | 1385 | 78 | 137888 | 100 | 1964877 | 647, 1, KB872443:19678-20972 | plot astMex1 | |
| 048 | 2013 | balAcu1 | GCF_000493695.1 | SOAPdenovo v. 16-Mar-2012 | 211 | 149 | 57860 | 821 | 371511 | 926, 15, KI537556:2252563-2254429 | plot balAcu1 | |
| 049 | 2014 | balPav1 | GCA_000709895.1 | SOAPdenovo v. 1.6 | 5 | 270 | 1303 | 216 | 1098 | 391, 46, KL482982:8685-9512 | plot balPav1 | |
| 050 | 2014 | bisBis1 | GCA_000754665.1 | MaSuRCA v. 2.1.0 | 8184 | 72 | 712109 | 100 | 947641 | 933, 100, KN265089v1:519297-521262 | plot bisBis1 | |
| 052 | 2011 | bosMut1 | GCA_000298355.1 | SOAPdenovo v. 1.14 | 139 | 83 | 27917 | 1274 | 256420 | 71, 14, JH880933:479978-480133 | plot bosMut1 | |
| 053 | 2004 | bosTau1 | tbd | tbd | 6550 | 40 | 289123 | 50 | 609155 | 200, 50, SCAFFOLD51732:9156-9605 | plot bosTau1 | |
| 054 | 2005 | bosTau2 | tbd | tbd | 4361 | 105 | 564259 | 50 | 2525381 | 997, 50, scaffold4383:34413-36456 | plot bosTau2 | |
| 055 | 2006 | bosTau3 | tbd | tbd | 411 | 51 | 38673 | 50 | 270212 | 1000, 50, chr10:68862764-68864813 | plot bosTau3 | |
| 056 | 2007 | bosTau4 | tbd | tbd | 437 | 53 | 52814 | 50 | 376407 | 1000, 50, chr10:75537624-75539673 | plot bosTau4 | |
| 057 | 2009 | bosTau5 | tbd | tbd | 435 | 53 | 51742 | 50 | 376650 | 1000, 50, chr10:75464684-75466733 | plot bosTau5 | |
| 058 | 2009 | bosTau6 | GCF_000003055.5 | UMD Overlapper v. 2009; additional processing | 789 | 670 | 463109 | 100 | 87080 | 923, 1, chr22:31476636-31478482 | plot bosTau6 | |
| 059 | 2011 | bosTau7 | tbd | tbd | 413 | 55 | 39706 | 50 | 141131 | 1000, 50, chr10:75201034-75203083 | plot bosTau7 | |
| 060 | 2014 | bosTau8 | GCF_000003055.5 | UMD Overlapper v. 2009; additional processing | 789 | 670 | 463109 | 100 | 87080 | 923, 1, chr22:31476636-31478482 | plot bosTau8 | |
| 061 | 2009 | bosTauMd3 | tbd | tbd | 789 | 670 | 463109 | 100 | 87080 | 923, 1, chr22:31476636-31478482 | plot bosTauMd3 | |
| 062 | 2006 | braFlo1 | tbd | tbd | 31 | 484 | 14260 | 417 | 12668 | 375, 1, chrUn:879323570-879324320 | plot braFlo1 | |
| 063 | 2008 | braFlo2 | tbd | tbd | 22 | 439 | 8529 | 411 | 9064 | 36, 1, Bf_V2_248:1229532-1229604 | plot braFlo2 | |
| 064 | 1880 | braRap1 | GCF_000309985.1 | SOAPdenovo v. 1.04 | 12 | 104 | 3193 | 2810 | 47557 | 587, 472, chrUn_JH977260:73788-75433 | plot braRap1 | |
| 065 | 2007 | bruMal1 | tbd | tbd | 55 | 50 | 6093 | 1 | 18780 | 87, 1, Bmal_supercontig14387:293-467 | plot bruMal1 | |
| 066 | 2014 | bruMal2 | tbd | tbd | 46 | 124.5 | 12221 | 431.5 | 63506 | 1000, 20, Bmal_v3_scaffold83:22898-24917 | plot bruMal2 | |
| 067 | 2013 | bubBub1 | GCF_000471725.1 | MaSuRCA v. 1.8.3 | 2383 | 163 | 395268 | 100 | 251657 | 990, 100, KI418684:2409965-2412044 | plot bubBub1 | |
| 068 | 2014 | bucRhi1 | GCF_000710305.1 | SOAPdenovo v. 1.6 | 31 | 114 | 5089 | 78 | 3263 | 327, 10, KL526600:8925-9588 | plot bucRhi1 | |
| 070 | 2011 | burXyl1 | tbd | tbd | 65 | 601 | 33110 | 301 | 19553 | 977, 300, scaffold00460:102617-104870 | plot burXyl1 | |
| 071 | 2010 | caeAng1 | GCA_000165025.1 | Velvet v. 0.7.56 | 414 | 41 | 16726 | 2 | 1802 | 46, 2, scafRNAPATH105:2285-2378 | plot caeAng1 | |
| 072 | 2012 | caeAng2 | tbd | tbd | 461 | 46 | 19505 | 2 | 1495 | 46, 2, Cang_2012_03_13_00008:384957-385050 | plot caeAng2 | |
| 073 | 2008 | caeJap1 | tbd | tbd | 135 | 58 | 10431 | 186 | 27893 | 687, 10, chrUn:37794313-37795696 | plot caeJap1 | |
| 074 | 2009 | caeJap2 | tbd | tbd | 765 | 103 | 130030 | 1018 | 891958 | 707, 10, chrUn:150512438-150513861 | plot caeJap2 | |
| 075 | 1880 | caeJap2a | tbd | tbd | 764 | 103 | 129273 | 1018 | 890958 | 707, 10, Cjap_Contig4853:3969-5392 | plot caeJap2a | |
| 077 | 2010 | caeJap4 | GCA_000147155.1 | Celera assembler v. 6.0 | 16 | 98.5 | 3188 | 20 | 1468 | 1000, 20, Scaffold17129:65445-67464 | plot caeJap4 | |
| 078 | 2007 | caePb1 | tbd | tbd | 115 | 44 | 9160 | 164 | 37674 | 476, 10, chrUn:52430125-52431086 | plot caePb1 | |
| 079 | 2008 | caePb2 | tbd | tbd | 83 | 37 | 3814 | 222 | 63681 | 230, 10, chrUn:74484521-74484990 | plot caePb2 | |
| 080 | 2010 | caePb3 | GCA_000143925.2 | PCAP v. 9/3/04 | 89 | 37 | 4915 | 222 | 74680 | 230, 10, Scfld02_75:384084-384553 | plot caePb3 | |
| 081 | 2005 | caeRem1 | tbd | tbd | 58 | 96 | 10213 | 133.5 | 11238 | 678, 10, SuperCont3:723391-724756 | plot caeRem1 | |
| 082 | 2006 | caeRem2 | tbd | tbd | 58 | 96 | 10213 | 133.5 | 11238 | 678, 10, chrUn:13919319-13920684 | plot caeRem2 | |
| 083 | 2007 | caeRem3 | tbd | tbd | 46 | 50 | 5760 | 197.5 | 14178 | 460, 10, chrUn:27560772-27561701 | plot caeRem3 | |
| 084 | 2007 | caeRem4 | GCF_000149515.1 | tbd | 46 | 50 | 5760 | 197.5 | 14178 | 460, 10, Crem_Contig253:25277-26206 | plot caeRem4 | |
| 085 | 2010 | caeSp111 | GCA_000186765.1 | Celera assembler v. 6.0 | 4 | 194.5 | 760 | 20 | 80 | 333, 20, Scaffold629:32984714-32985399 | plot caeSp111 | |
| 086 | 2012 | caeSp51 | tbd | tbd | 14 | 34 | 730 | 12.5 | 894 | 201, 3, Csp5_scaffold_09411:792-1196 | plot caeSp51 | |
| 087 | 2010 | caeSp71 | tbd | tbd | 535 | 47 | 30250 | 213 | 312209 | 162, 20, Scaffold11:29462-29805 | plot caeSp71 | |
| 088 | 2010 | caeSp91 | tbd | tbd | 26 | 217.5 | 7172 | 8745 | 180575 | 1000, 20, Scaffold7498:303469-305488 | plot caeSp91 | |
| 089 | 2014 | calAnn1 | GCF_000699085.1 | SOAPdenovo v. 1.6 | 89 | 127 | 16337 | 1006 | 168943 | 440, 38, KL218155:301090-302007 | plot calAnn1 | |
| 090 | 2007 | calJac1 | tbd | tbd | 1597 | 42 | 129367 | 182 | 377725 | 937, 10, Contig4771:110891-112774 | plot calJac1 | |
| 091 | 2009 | calJac3 | GCF_000004665.1 | PCAP v. 2009 | 1516 | 43 | 116646 | 183.5 | 452860 | 807, 10, chr3:111956760-111958383 | plot calJac3 | |
| 092 | 2013 | calMil1 | GCF_000165045.1 | Celera v. 6.1 | 31 | 123 | 8335 | 100 | 70257 | 1000, 100, KI635945:3331497-3333596 | plot calMil1 | |
| 093 | 2011 | camFer1 | GCF_000311805.1 | SOAPdenovo v. V1.05 | 11 | 205 | 2059 | 129 | 2031 | 237, 2, KB018701:319294-319769 | plot camFer1 | |
| 094 | 2004 | canFam1 | tbd | tbd | 12 | 153 | 2669 | 210.5 | 8118 | 104, 1, chr18:45376349-45376557 | plot canFam1 | |
| 095 | 2005 | canFam2 | tbd | tbd | 32 | 199.5 | 8095 | 1 | 5245 | 746, 1, chrUn:76334072-76335564 | plot canFam2 | |
| 096 | 2011 | canFam3 | GCF_000002285.3 | Arachne v. April 2010 | 34 | 175.5 | 8234 | 10 | 4545 | 746, 10, chrUn_JH374132:3424-4925 | plot canFam3 | |
| 099 | 2014 | capCar1 | GCF_000700745.1 | SOAPdenovo v. 1.6 | 4 | 105 | 618 | 48 | 354 | 139, 26, KL359104:23556-23859 | plot capCar1 | |
| 100 | 2012 | capHir1 | GCF_000317765.1 | SOAPdenovo v. 1.03 | 627 | 41 | 71810 | 100 | 546475 | 988, 16, chr16:40339512-40341503 | plot capHir1 | |
| 101 | 2014 | carCri1 | GCF_000690535.1 | SOAPdenovo v. 1.6 | 4 | 161 | 644 | 210.5 | 878 | 52, 13, KK509558:67998-68114 | plot carCri1 | |
| 102 | 2005 | cavPor2 | tbd | tbd | 393 | 427 | 164744 | 100 | 166667 | 986, 100, scaffold_291164:123135-125206 | plot cavPor2 | |
| 103 | 2008 | cavPor3 | GCF_000151735.1 | unknown v. before 2008 | 3 | 145 | 552 | 100 | 961 | 313, 100, scaffold_799:9280-10005 | plot cavPor3 | |
| 104 | 2002 | cb1 | tbd | tbd | 81 | 163 | 20408 | 145 | 39126 | 645, 10, chrUn:51532611-51533910 | plot cb1 | |
| 105 | 2005 | cb2 | tbd | tbd | 86 | 153 | 21033 | 163.5 | 42461 | 645, 10, chrI:9244132-9245431 | plot cb2 | |
| 106 | 2007 | cb3 | tbd | tbd | 80 | 148.5 | 19176 | 166.5 | 39580 | 645, 10, chrI:9355978-9357277 | plot cb3 | |
| 107 | 2011 | cb4 | tbd | tbd | 86 | 153 | 20969 | 151.5 | 40114 | 645, 10, chrI:11247250-11248549 | plot cb4 | |
| 118 | 2012 | cerSim1 | GCF_000283155.1 | ALLPATHS v. R41370 | 1818 | 68 | 129697 | 100 | 270005 | 815, 100, JH767775:6384924-6386653 | plot cerSim1 | |
| 119 | 2014 | chaVoc1 | GCF_000708025.1 | SOAPdenovo v. 1.6 | 47 | 200 | 13700 | 1514 | 133699 | 780, 257, KL409415:13594818-13596634 | plot chaVoc1 | |
| 120 | 2014 | chaVoc2 | GCF_000708025.1 | SOAPdenovo v. 1.6 | 47 | 200 | 13700 | 1514 | 133699 | 780, 257, KL873469:13594818-13596634 | plot chaVoc2 | |
| 121 | 2013 | cheMyd1 | GCF_000344595.1 | SOAPdenovo v. 1.05 | 129 | 204 | 37111 | 798 | 277853 | 314, 27, KB535131:1778822-1779476 | plot cheMyd1 | |
| 122 | 2012 | chiLan1 | GCA_000276665.1 | ALLPATHS v. R40776 | 1183 | 70 | 101029 | 100 | 267937 | 996, 100, JH721987:2542897-2544988 | plot chiLan1 | |
| 123 | 2013 | chlSab1 | tbd | tbd | 23634 | 81 | 2123928 | 10 | 396229 | 923, 1, chrX:117110178-117112024 | plot chlSab1 | |
| 124 | 2014 | chlSab2 | GCF_000409795.2 | ALLPATHS and Newbler v. 13-Feb-2013 | 23631 | 81 | 2123656 | 10 | 396199 | 923, 1, chrX:117110178-117112024 | plot chlSab2 | |
| 125 | 2014 | chlUnd1 | GCF_000695195.1 | SOAPdenovo v. 1.6 | 5 | 293 | 1223 | 129 | 617 | 310, 65, KK747264:28313-28997 | plot chlUnd1 | |
| 126 | 2008 | choHof1 | GCA_000164785.1 | tbd | 104 | 54.5 | 14520 | 145.5 | 33892 | 986, 100, scaffold_56240:3133-5204 | plot choHof1 | |
| 127 | 2012 | chrAsi1 | GCF_000296735.1 | allpaths v. R42316 HAPLOIDIFY=True | 3416 | 76 | 339291 | 100 | 720504 | 991, 100, JH823765:402000-404081 | plot chrAsi1 | |
| 128 | 2011 | chrPic1 | tbd | tbd | 7555 | 79 | 738667 | 50 | 1230115 | 64, 1, JH584466:5301285-5301413 | plot chrPic1 | |
| 129 | 2014 | chrPic2 | GCA_000241765.2 | Newbler v. 2.6 | 6315 | 77 | 629230 | 206 | 2593694 | 1000, 10, chrUn_KK083066v1:1300793-1302802 | plot chrPic2 | |
| 130 | 2002 | ci1 | GCA_000183065.1 | tbd | 28 | 311.5 | 8955 | 50 | 11060 | 833, 50, Scaffold_7:289989-291704 | plot ci1 | |
| 131 | 2005 | ci2 | tbd | tbd | 2 | 472.5 | 945 | 173 | 346 | 843, 296, scaffold_403:40134-42115 | plot ci2 | |
| 132 | 2011 | ci3 | GCF_000224145.1 | tbd | 22 | 258.5 | 6455 | 50 | 9493 | 597, 50, chrUn_NW_004190451v1:5050-6293 | plot ci3 | |
| 133 | 2003 | cioSav1 | tbd | tbd | 8 | 124 | 1554 | 100 | 2755 | 296, 100, ps_146:263977-264668 | plot cioSav1 | |
| 134 | 2005 | cioSav2 | tbd | tbd | 6 | 402.5 | 2394 | 200 | 1668 | 636, 10, reftig_72:2536022-2537303 | plot cioSav2 | |
| 135 | 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 | |
| 136 | 2013 | colLiv1 | GCF_000337935.1 | SOAPdenovo v. 2.0 | 19 | 116 | 3824 | 1290 | 32865 | 33, 57, KB379196:2050-2172 | plot colLiv1 | |
| 137 | 2014 | colStr1 | GCF_000690715.1 | SOAPdenovo v. 1.6 | 5 | 161 | 910 | 308 | 1203 | 362, 113, KK530485:3407-4243 | plot colStr1 | |
| 138 | 2012 | conCri1 | GCF_000260355.1 | AllPaths v. 2012 | 1110 | 72 | 108033 | 100 | 233431 | 924, 100, JH655880:49229854-49231801 | plot conCri1 | |
| 139 | 2014 | corBra1 | GCF_000691975.1 | SOAPdenovo v. 1.6 | 41 | 90 | 7520 | 1445 | 112176 | 259, 28, KK718436:193091-193636 | plot corBra1 | |
| 140 | 2014 | corCor1 | GCF_000738735.1 | AllPaths v. Allpaths-LG version 41687 | 21 | 81 | 2189 | 1027 | 27602 | 81, 1, KL997637:955359-955521 | plot corCor1 | |
| 141 | 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 | |
| 142 | 2013 | criGri1 | GCF_000419365.1 | SOAPdenovo v. 2.2 | 588 | 217 | 196516 | 1481.5 | 1359815 | 422, 10, KE379019:554914-555767 | plot criGri1 | |
| 143 | 2011 | criGriChoV1 | GCF_000223135.1 | SOAPdenovo v. 1.05 | 213 | 162 | 53736 | 1526 | 472877 | 369, 10, NW_003615838v1:158557-159304 | plot criGriChoV1 | |
| 144 | 2014 | cucCan1 | GCF_000709325.1 | SOAPdenovo v. 1.6 | 113 | 242 | 41656 | 972 | 203191 | 961, 69, KL448150:311854-313844 | plot cucCan1 | |
| 145 | 2014 | cynSem1 | GCF_000523025.1 | SOAPdenovo v. April-2011 | 78 | 311.5 | 27891 | 935.5 | 165198 | 568, 38, chr11:13981930-13983103 | plot cynSem1 | |
| 146 | 2014 | cypVar1 | GCA_000732505.1 | AllPaths v. May 2014 | 3240 | 89 | 423504 | 1 | 2210432 | 1000, 1, KL653732:89449-91449 | plot cypVar1 | |
| 147 | 2003 | danRer1 | tbd | tbd | 1280 | 57 | 186413 | 10 | 322061 | 1000, 10, chr25:16217228-16219237 | plot danRer1 | |
| 148 | 2014 | danRer10 | GCF_000002035.5 | tbd | 575 | 174 | 105525 | 10 | 17550 | 484, 10, chr5:1032421-1033398 | plot danRer10 | |
| 149 | 2004 | danRer2 | tbd | tbd | 1150 | 58 | 191859 | 10 | 223764 | 1000, 10, chr10:26174984-26176993 | plot danRer2 | |
| 150 | 2005 | danRer3 | tbd | tbd | 819 | 58 | 88143 | 10 | 121196 | 776, 10, chrUn:112388525-112390086 | plot danRer3 | |
| 151 | 2006 | danRer4 | tbd | tbd | 726 | 65.5 | 121967 | 14 | 135012 | 705, 11, chr25:30060270-30061690 | plot danRer4 | |
| 152 | 2007 | danRer5 | tbd | tbd | 1559 | 170 | 288298 | 100 | 155702 | 73, 1, chr21:35548773-35548919 | plot danRer5 | |
| 153 | 2008 | danRer6 | tbd | tbd | 1421 | 133 | 225674 | 100 | 142101 | 1000, 100, Zv8_scaffold431:54613-56712 | plot danRer6 | |
| 154 | 2010 | danRer7 | GCF_000002035.4 | tbd | 1245 | 164 | 217595 | 100 | 124500 | 900, 100, chr22:2241720-2243619 | plot danRer7 | |
| 155 | 2005 | dasNov1 | tbd | tbd | 55 | 123 | 12971 | 111 | 31368 | 681, 100, scaffold_3005:3743-5204 | plot dasNov1 | |
| 156 | 2008 | dasNov2 | tbd | tbd | 109 | 136 | 25865 | 100 | 58752 | 836, 100, scaffold_3394:70496-72267 | plot dasNov2 | |
| 157 | 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 | |
| 158 | 2014 | dicLab1 | GCA_000689215.1 | tbd | 275 | 423 | 116519 | 203 | 134149 | 994, 20, HG916850:2956140-2958147 | plot dicLab1 | |
| 159 | 2008 | dipOrd1 | GCA_000151885.1 | tbd | 219 | 46 | 46012 | 379 | 102683 | 1000, 100, scaffold_2463:9467-11566 | plot dipOrd1 | |
| 160 | 2013 | dirImm1 | tbd | tbd | 505 | 175 | 132528 | 2 | 32073 | 999, 1, nDi_2_2_scaf00035:47420-49418 | plot dirImm1 | |
| 161 | 2003 | dm1 | tbd | tbd | 9 | 252 | 2984 | 20 | 1237 | 604, 20, chrU:5250525-5251752 | plot dm1 | |
| 162 | 2004 | dm2 | tbd | tbd | 8 | 362 | 2818 | 20 | 1217 | 604, 20, chrU:5250525-5251752 | plot dm2 | |
| 163 | 2006 | dm3 | tbd | tbd | 20 | 286 | 4907 | 100 | 423940 | 276, 20, chrU:4943122-4943693 | plot dm3 | |
| 164 | 2014 | dm6 | GCF_000001215.4 | tbd | 15 | 333 | 4828 | 100 | 1340 | 276, 20, chrUn_DS483709v1:12934-13505 | plot dm6 | |
| 165 | 2003 | dp2 | tbd | tbd | 113 | 64 | 11633 | 10 | 9049 | 784, 10, Contig4969_Contig4496:202614-204191 | plot dp2 | |
| 166 | 2004 | dp3 | tbd | tbd | 136 | 79.5 | 17354 | 79.5 | 14988 | 485, 11, chrU:7044759-7045739 | plot dp3 | |
| 167 | 2006 | dp4 | tbd | tbd | 183 | 81 | 19720 | 50 | 18528 | 798, 50, chrXL_group1e:8376310-8377955 | plot dp4 | |
| 168 | 2012 | droAlb1 | GCA_000298335.1 | SOAPdenovo v. 1.04 | 4360 | 30 | 131320 | 22 | 152454 | 76, 1, JH853217:889-1041 | plot droAlb1 | |
| 169 | 2004 | droAna1 | tbd | tbd | 103 | 252 | 28853 | 100 | 10300 | 943, 100, 2448822:95133-97118 | plot droAna1 | |
| 170 | 2005 | droAna2 | tbd | tbd | 32 | 160 | 7905 | 701 | 72786 | 791, 25, scaffold_13266:420335-421941 | plot droAna2 | |
| 171 | 2006 | droAna3 | GCF_000005115.1 | tbd | 35 | 143 | 8663 | 671 | 75001 | 707, 25, scaffold_13230:483470-484908 | plot droAna3 | |
| 172 | 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 | |
| 173 | 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 | |
| 174 | 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 | |
| 175 | 2005 | droEre1 | tbd | tbd | 8 | 86.5 | 1545 | 731 | 6855 | 773, 25, scaffold_4784:23686196-23687766 | plot droEre1 | |
| 176 | 2006 | droEre2 | GCF_000005135.1 | tbd | 14 | 221 | 4384 | 239 | 7433 | 763, 25, scaffold_4784:18133045-18134595 | plot droEre2 | |
| 177 | 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 | |
| 178 | 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 | |
| 179 | 2005 | droGri1 | tbd | tbd | 17 | 76 | 2908 | 444 | 11143 | 734, 312, scaffold_24659:1579-3358 | plot droGri1 | |
| 180 | 2006 | droGri2 | GCF_000005155.2 | tbd | 48 | 60.5 | 5904 | 430.5 | 52107 | 774, 25, scaffold_15245:16809148-16810720 | plot droGri2 | |
| 181 | 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 | |
| 182 | 2013 | droMir2 | GCA_000269505.2 | Newbler v. 2.6 | 122 | 72 | 16465 | 10 | 57520 | 1000, 10, chr2:9770771-9772780 | plot droMir2 | |
| 184 | 2005 | droMoj2 | tbd | tbd | 22 | 219.5 | 7748 | 366.5 | 30847 | 969, 25, scaffold_6496:4573125-4575087 | plot droMoj2 | |
| 185 | 2006 | droMoj3 | GCF_000005175.2 | tbd | 16 | 343 | 6118 | 426 | 29359 | 859, 25, scaffold_6496:14181729-14183471 | plot droMoj3 | |
| 186 | 2005 | droPer1 | GCF_000005195.2 | tbd | 28 | 402 | 10502 | 100 | 10914 | 937, 100, super_12:105769-107742 | plot droPer1 | |
| 187 | 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 | |
| 188 | 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 | |
| 189 | 2005 | droSec1 | GCA_000005215.1 | tbd | 17 | 399 | 6822 | 100 | 5318 | 765, 100, super_59:77146-78775 | plot droSec1 | |
| 190 | 2005 | droSim1 | tbd | tbd | 109 | 106 | 23001 | 298 | 40703 | 801, 10, chr2L:4623692-4625303 | plot droSim1 | |
| 191 | 2014 | droSim2 | GCF_000754195.2 | Velvet v. 1.1.04 | 104 | 58 | 5999 | 10 | 1818 | 359, 8, chr2R:7425888-7426613 | plot droSim2 | |
| 192 | 2013 | droSuz1 | GCA_000472105.1 | SOAPdenovo v. 2 | 71 | 185 | 16489 | 1565 | 196054 | 364, 76, KI420423:11753-12556 | plot droSuz1 | |
| 193 | 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 | |
| 194 | 2004 | droVir1 | tbd | tbd | 48 | 328.5 | 15839 | 25 | 16648 | 698, 25, scaffold_10:2740496-2741916 | plot droVir1 | |
| 195 | 2005 | droVir2 | tbd | tbd | 13 | 232 | 3421 | 1415 | 46365 | 503, 25, scaffold_13324:149342-150372 | plot droVir2 | |
| 196 | 2006 | droVir3 | GCF_000005245.1 | tbd | 12 | 341 | 4206 | 1536.5 | 45200 | 423, 25, scaffold_13324:149231-150101 | plot droVir3 | |
| 197 | 2006 | droWil1 | GCF_000005925.1 | tbd | 23 | 248 | 8712 | 1330 | 51159 | 759, 50, scaffold_181150:697726-699293 | plot droWil1 | |
| 198 | 2006 | droWil2 | GCF_000005925.1 | tbd | 23 | 248 | 8712 | 1330 | 51159 | 759, 50, CH964291:697726-699293 | plot droWil2 | |
| 199 | 2004 | droYak1 | tbd | tbd | 65 | 340 | 25549 | 250 | 24358 | 955, 50, chrU:40768288-40770247 | plot droYak1 | |
| 200 | 2005 | droYak2 | tbd | tbd | 99 | 170 | 26922 | 54 | 37713 | 684, 10, chr2L:22155365-22156742 | plot droYak2 | |
| 201 | 2006 | droYak3 | GCF_000005975.2 | tbd | 85 | 143 | 20479 | 10 | 23713 | 684, 10, chr2L:22155365-22156742 | plot droYak3 | |
| 204 | 2005 | echTel1 | tbd | tbd | 89 | 83 | 17114 | 100 | 22024 | 805, 100, scaffold_272928:13200-14909 | plot echTel1 | |
| 205 | 2012 | echTel2 | GCF_000313985.1 | ALLPATHS v. R37599 | 3871 | 93 | 620444 | 100 | 656358 | 998, 100, JH980317:1376657-1378752 | plot echTel2 | |
| 206 | 2014 | egrGar1 | GCF_000687185.1 | SOAPdenovo v. 1.6 | 112 | 213.5 | 33121 | 1093.5 | 229589 | 998, 134, KK502338:445846-447975 | plot egrGar1 | |
| 207 | 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 | |
| 208 | 2012 | eleEdw1 | GCF_000299155.1 | allpaths v. R42301 HAPLOIDIFY=True | 1643 | 71 | 141553 | 100 | 311199 | 1000, 100, JH947463:2106240-2108339 | plot eleEdw1 | |
| 209 | 2012 | eptFus1 | GCF_000308155.1 | ALLPATHS v. R40371 | 1641 | 75 | 188916 | 100 | 378407 | 988, 100, JH977647:11513546-11515621 | plot eptFus1 | |
| 210 | 2007 | equCab1 | tbd | tbd | 17 | 457 | 5982 | 100 | 6200 | 715, 100, chr2:10720193-10721722 | plot equCab1 | |
| 211 | 2007 | equCab2 | tbd | tbd | 4 | 160.5 | 610 | 1909 | 18507 | 258, 295, chr22:17653073-17653883 | plot equCab2 | |
| 212 | 2014 | equPrz1 | GCA_000696695.1 | SOAPdenovo v. 1.05 | 39 | 49 | 5163 | 49 | 12408 | 78, 11, KK955445:38997-39163 | plot equPrz1 | |
| 213 | 2006 | eriEur1 | tbd | tbd | 343 | 435 | 146738 | 100 | 209198 | 1000, 100, scaffold_366352:52823-54922 | plot eriEur1 | |
| 214 | 2012 | eriEur2 | GCF_000296755.1 | allpaths v. R41008 | 3596 | 70 | 265454 | 100 | 1205265 | 1000, 100, JH835375:3514396-3516495 | plot eriEur2 | |
| 215 | 2014 | esoLuc1 | GCA_000721915.1 | AllPaths v. 43500 | 9785 | 81 | 734131 | 15 | 1227519 | 950, 10, LG19:14032217-14034126 | plot esoLuc1 | |
| 217 | 2014 | eurHel1 | GCF_000690775.1 | SOAPdenovo v. 1.6 | 2 | 89.5 | 179 | 436 | 872 | 113, 451, KK569808:53808-54484 | plot eurHel1 | |
| 219 | 2013 | falChe1 | GCF_000337975.1 | SOAPdenovo v. 1.4 | 27 | 206 | 7614 | 685 | 35918 | 51, 10, KB397780:7020361-7020472 | plot falChe1 | |
| 220 | 2013 | falPer1 | GCF_000337955.1 | SOAPdenovo v. 1.4 | 6 | 48.5 | 530 | 631.5 | 4836 | 36, 10, KB391040:3398436-3398517 | plot falPer1 | |
| 221 | 1880 | felCat1 | tbd | tbd | 1343 | 353 | 504058 | 874 | 2708782 | 1000, 100, scaffold_217423:45453-47552 | plot felCat1 | |
| 222 | 2006 | felCat3 | tbd | tbd | 1343 | 353 | 504058 | 874 | 2708782 | 1000, 100, scaffold_217423:45453-47552 | plot felCat3 | |
| 223 | 2008 | felCat4 | GCA_000003115.1 | tbd | 9736 | 503 | 4582767 | 10 | 9398414 | 1000, 10, chrA2:8725380-8727389 | plot felCat4 | |
| 224 | 2011 | felCat5 | GCF_000181335.1 | Celera Assembler v. 6.1 | 27 | 72 | 6437 | 20 | 100569 | 488, 20, chrB2:22462351-22463346 | plot felCat5 | |
| 225 | 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 | |
| 226 | 2013 | ficAlb2 | GCF_000247815.1 | SOAPdenovo v. 1.05 | 632 | 77 | 75592 | 40.5 | 206854 | 982, 1, chr7:28154426-28156390 | plot ficAlb2 | |
| 227 | 2002 | fr1 | tbd | tbd | 76 | 155.5 | 19306 | 50 | 16684 | 71, 1, chrUn:149577204-149577346 | plot fr1 | |
| 228 | 2004 | fr2 | tbd | tbd | 5 | 313 | 1682 | 512 | 2231 | 47, 1, chrUn:336404518-336404612 | plot fr2 | |
| 229 | 2011 | fr3 | GCF_000180615.1 | tbd | 6 | 229 | 1827 | 286 | 2291 | 47, 1, HE592038:5063-5157 | plot fr3 | |
| 230 | 2014 | fulGla1 | GCF_000690835.1 | SOAPdenovo v. 1.6 | 8 | 336.5 | 2583 | 103.5 | 1637 | 450, 20, KK597768:8602-9521 | plot fulGla1 | |
| 231 | 2010 | gadMor1 | GCA_000231765.1 | tbd | 168 | 53 | 11363 | 270 | 70748 | 51, 1, CAEA01526699:46-148 | plot gadMor1 | |
| 232 | 2004 | galGal2 | tbd | tbd | 114 | 40 | 12930 | 124 | 17674 | 778, 21, chr3:68417113-68418689 | plot galGal2 | |
| 233 | 2006 | galGal3 | tbd | tbd | 729 | 37 | 34199 | 500 | 325853 | 479, 10, chrUn_random:55035794-55036761 | plot galGal3 | |
| 234 | 2011 | galGal4 | GCF_000002315.3 | Celera Assembler v. 5.4 | 55 | 401 | 22946 | 100 | 31537 | 805, 100, chr19:3903221-3904930 | plot galGal4 | |
| 235 | 2015 | galGal5 | GCF_000002315.4 | MHAP/PBcR v. 8.2beta | 1 | 33 | 33 | 795 | 795 | 33, 795, chrUn_NT_465606v1:9086-9946 | plot galGal5 | |
| 236 | 2014 | galVar1 | GCF_000696425.1 | SOAPdenovo2 v. April 2014 | 58964 | 61 | 5626241 | 419 | 24866346 | 997, 1, NW_007727116v1:311725-313719 | plot galVar1 | |
| 237 | 2006 | gasAcu1 | tbd | tbd | 8 | 46.5 | 1970 | 117.5 | 2520 | 841, 100, chrUn:38727446-38729227 | plot gasAcu1 | |
| 239 | 2009 | gavGan0 | tbd | tbd | 30236 | 134 | 5187944 | 5000 | 145799649 | 915, 10, scaffold24725:12789-14628 | plot gavGan0 | |
| 240 | 2014 | gavSte1 | GCF_000690875.1 | SOAPdenovo v. 1.6 | 5 | 164 | 848 | 318 | 2312 | 269, 245, KK640233:828-1610 | plot gavSte1 | |
| 241 | 2012 | geoFor1 | GCF_000277835.1 | SOAPdenovo v. 2.01 | 32 | 105.5 | 4877 | 945.5 | 51025 | 617, 11, JH739922:1318693-1319937 | plot geoFor1 | |
| 243 | 2009 | gorGor2 | tbd | tbd | 6585 | 247 | 2365617 | 10 | 499615 | 1000, 10, chr10_101645027_418909:206049-208058 | plot gorGor2 | |
| 244 | 2011 | gorGor3 | GCF_000151905.1 | tbd | 6926 | 246 | 2475426 | 10 | 533805 | 1000, 10, chr10:101539188-101541197 | plot gorGor3 | |
| 245 | 2014 | gorGor4 | GCA_000151905.3 | tbd | 8691 | 94 | 1514940 | 25 | 982883 | 246, 1, chr9:24397320-24397812 | plot gorGor4 | |
| 247 | 2009 | haeCon1 | tbd | tbd | 25 | 39 | 1031 | 10 | 1745 | 58, 10, Hcon_Contig0056815:13389-13514 | plot haeCon1 | |
| 248 | 2013 | haeCon2 | tbd | tbd | 5378 | 149 | 831727 | 55 | 351011 | 700, 1, scaffold_63:260903-262303 | plot haeCon2 | |
| 249 | 2014 | halAlb1 | GCF_000691405.1 | SOAPdenovo v. 1.6 | 11 | 126 | 1936 | 370 | 3807 | 466, 102, KK641449:26277-27310 | plot halAlb1 | |
| 250 | 2014 | halLeu1 | GCF_000737465.1 | SOAPdenovo2 v. May 2014 | 14 | 280 | 4342 | 95 | 1676 | 194, 10, KL869356:8708537-8708934 | plot halLeu1 | |
| 251 | 2011 | hapBur1 | GCF_000239415.1 | ALLPATHS-LG v. R35951 | 965 | 95 | 135908 | 20 | 374038 | 975, 20, JH425754:7557-9526 | plot hapBur1 | |
| 252 | 2011 | hetBac1 | GCA_000223415.1 | Celera assembler v. 6.0 | 3 | 228 | 1282 | 20 | 60 | 1000, 20, GL996479v1:885362-887381 | plot hetBac1 | |
| 253 | 2011 | hetGla1 | tbd | tbd | 743 | 313 | 285174 | 1994 | 2914751 | 785, 43, JH165660:4306-5918 | plot hetGla1 | |
| 254 | 2012 | hetGla2 | GCF_000247695.1 | AllPaths v. R39605 | 595 | 70 | 44604 | 100 | 201552 | 1000, 100, JH602085:17402968-17405067 | plot hetGla2 | |
| 255 | 2009 | hg19 | tbd | tbd | 1 | 200 | 200 | 3000000 | 3000000 | 200, 3000000, chrY:10104354-13104753 | plot hg19 | |
| 256 | 2013 | hg38 | GCF_000001405.26 | tbd | 12 | 78 | 974 | 440 | 56689 | 125, 20, chrUn_KI270442v1:175618-175887 | plot hg38 | |
| 259 | 2012 | jacJac1 | GCF_000280705.1 | ALLPATHS v. R41689 HAPLOIDIFY=True | 2666 | 63 | 196366 | 100 | 569918 | 1000, 100, JH725440:52488719-52490818 | plot jacJac1 | |
| 260 | 2011 | latCha1 | GCF_000225785.1 | AllPaths v. R36819 | 2038 | 77 | 159059 | 100 | 504858 | 955, 100, JH127253:476850-478859 | plot latCha1 | |
| 262 | 2014 | lepDis1 | GCF_000691785.1 | SOAPdenovo v. 1.6 | 1 | 50 | 50 | 229 | 229 | 50, 229, KK681583:9399-9727 | plot lepDis1 | |
| 263 | 2011 | lepOcu1 | GCF_000242695.1 | AllPaths v. R38293 | 2079 | 95 | 232474 | 100 | 466733 | 1000, 100, chrLG4:37780111-37782210 | plot lepOcu1 | |
| 264 | 2013 | lepWed1 | GCF_000349705.1 | allpaths v. R41856 HAPLOIDIFY=True | 2022 | 63 | 135843 | 100 | 1218867 | 1000, 100, KB715312:1023296-1025395 | plot lepWed1 | |
| 265 | 2013 | letCam1 | GCA_000466285.1 | Newbler v. 2.7 | 1453 | 69 | 123952 | 100 | 739039 | 280, 39, KE994354:70338-70936 | plot letCam1 | |
| 266 | 1880 | linHum0 | GCF_000217595.1 | CABOG v. 5.3 | 179 | 48 | 10176 | 100 | 20986 | 480, 100, NW_012159984:28893-29952 | plot linHum0 | |
| 267 | 2013 | lipVex1 | GCF_000442215.1 | SOAPdenovo v. 2.01 | 292 | 92 | 66483 | 985.5 | 386576 | 876, 10, KE557659:158624-160385 | plot lipVex1 | |
| 268 | 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 | |
| 269 | 2005 | loxAfr1 | tbd | tbd | 79 | 44 | 11426 | 206 | 80801 | 687, 284, scaffold_10531:71539-73196 | plot loxAfr1 | |
| 270 | 2008 | loxAfr2 | tbd | tbd | 78 | 165.5 | 20735 | 1078 | 180887 | 989, 100, scaffold_3386:17920-19997 | plot loxAfr2 | |
| 271 | 2009 | loxAfr3 | GCF_000001905.1 | tbd | 11 | 45 | 1924 | 398 | 9784 | 731, 100, scaffold_211:333226-334787 | plot loxAfr3 | |
| 272 | 2007 | macEug1 | tbd | tbd | 7319 | 57 | 504656 | 10 | 562759 | 146, 1, Scaffold27901:25044-25336 | plot macEug1 | |
| 273 | 2009 | macEug2 | GCA_000004035.1 | tbd | 11689 | 55 | 752361 | 50 | 1102638 | 146, 1, GL058785:13153-13445 | plot macEug2 | |
| 274 | 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 | |
| 275 | 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 | |
| 276 | 2014 | manPen1 | GCA_000738955.1 | SOAPdenovo v. May 2014 | 37129 | 101 | 5536376 | 1 | 13090743 | 1000, 1, KN006700:349054-351054 | plot manPen1 | |
| 277 | 2014 | manVit1 | GCF_000692015.1 | SOAPdenovo v. 1.6 | 25 | 231 | 8844 | 1303 | 65245 | 701, 296, KK732740:655429-657126 | plot manVit1 | |
| 279 | 2012 | mayZeb1 | GCF_000238955.1 | AllPaths v. R37043 | 1831 | 95 | 241336 | 100 | 682313 | 1000, 100, JH720538:3252564-3254663 | plot mayZeb1 | |
| 280 | 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 | |
| 281 | 2009 | melGal1 | tbd | tbd | 834 | 127 | 136229 | 100 | 661041 | 169, 1, chr3:54352580-54352918 | plot melGal1 | |
| 282 | 2014 | melGal5 | GCF_000146605.2 | MaSuRCA v. 1.9.2 | 84 | 181 | 17431 | 100 | 76065 | 724, 100, chrZ:7873702-7875249 | plot melGal5 | |
| 285 | 2008 | melInc2 | tbd | tbd | 3 | 77 | 211 | 201 | 513 | 98, 201, MiV1ctg3:286050-286446 | plot melInc2 | |
| 286 | 2011 | melUnd1 | GCF_000238935.1 | Celera v. 6.1 | 39 | 89 | 5925 | 41 | 36796 | 334, 20, JH556232:114057-114744 | plot melUnd1 | |
| 287 | 2014 | merNub1 | GCF_000691845.1 | SOAPdenovo v. 1.6 | 2 | 154.5 | 309 | 361 | 722 | 245, 311, KK701714:10568-11368 | plot merNub1 | |
| 288 | 2013 | mesAur1 | GCF_000349665.1 | allpaths v. R44683 | 3589 | 71 | 248381 | 100 | 755166 | 212, 100, KB708269:3930600-3931123 | plot mesAur1 | |
| 289 | 2014 | mesUni1 | GCF_000695765.1 | SOAPdenovo v. 1.6 | 4 | 347 | 1434 | 124.5 | 451 | 332, 23, KK817080:7082-7768 | plot mesUni1 | |
| 290 | 1880 | micMur0 | tbd | tbd | 295 | 256 | 90483 | 780 | 749299 | 997, 100, GeneScaffold_4747:166512-168605 | plot micMur0 | |
| 291 | 2007 | micMur1 | GCA_000165445.1 | tbd | 124 | 124.5 | 33320 | 952.5 | 207469 | 969, 100, scaffold_5185:107104-109141 | plot micMur1 | |
| 292 | 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 | |
| 293 | 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 | |
| 294 | 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 | |
| 295 | 2011 | mm10 | tbd | tbd | 2 | 390.5 | 781 | 25879.5 | 51759 | 477, 1759, chrX_GL456233_random:239940-242652 | plot mm10 | |
| 296 | 1880 | mm5 | tbd | tbd | 204 | 48.5 | 30180 | 100 | 76884 | 921, 100, chr6:132460596-132462537 | plot mm5 | |
| 297 | 2005 | mm6 | tbd | tbd | 117 | 48 | 17647 | 100 | 48212 | 768, 100, chr14:100566071-100567706 | plot mm6 | |
| 298 | 2005 | mm7 | tbd | tbd | 45 | 48 | 5475 | 100 | 64491 | 451, 100, chr15:68974498-68975499 | plot mm7 | |
| 299 | 2006 | mm8 | tbd | tbd | 6 | 161 | 1257 | 162.5 | 50878 | 520, 353, chr14:87009574-87010966 | plot mm8 | |
| 300 | 2007 | mm9 | tbd | tbd | 2 | 390.5 | 781 | 25879.5 | 51759 | 477, 1759, chrX_random:239940-242652 | plot mm9 | |
| 301 | 2004 | monDom1 | tbd | tbd | 18 | 53.5 | 1891 | 127 | 11341 | 696, 100, scaffold_14754:178069-179560 | plot monDom1 | |
| 302 | 2005 | monDom2 | tbd | tbd | 5 | 428 | 2012 | 100 | 520 | 870, 100, scaffold_38:23849795-23851634 | plot monDom2 | |
| 303 | 2006 | monDom4 | tbd | tbd | 9 | 183 | 3070 | 1000 | 21732 | 870, 1, chr1:400420041-400421781 | plot monDom4 | |
| 304 | 2006 | monDom5 | tbd | tbd | 9 | 183 | 3070 | 1000 | 21732 | 870, 1, chr1:424248968-424250708 | plot monDom5 | |
| 305 | 2013 | musDom2 | GCF_000371365.1 | AllPathsLG v. September 2012 | 1284 | 85 | 165577 | 1 | 473996 | 1000, 1, KB855954:134298-136298 | plot musDom2 | |
| 306 | 2011 | musFur1 | GCA_000215625.1 | ALLPATHS-LG v. R36167 | 1009 | 84 | 107706 | 44 | 286510 | 1000, 20, GL897138:9717-11736 | plot musFur1 | |
| 307 | 2013 | myoBra1 | GCF_000412655.1 | SOAP de novo v. 2.04 | 356 | 119 | 85889 | 1109 | 766318 | 1000, 31, KE163605:2655193-2657223 | plot myoBra1 | |
| 308 | 2012 | myoDav1 | GCF_000327345.1 | SOAPdenovo v. 1.06 | 303 | 151 | 56967 | 1283 | 942238 | 502, 19, KB106370:3092722-3093744 | plot myoDav1 | |
| 309 | 2006 | myoLuc1 | tbd | tbd | 42 | 47 | 6392 | 1551 | 125787 | 388, 100, scaffold_150441:136761-137636 | plot myoLuc1 | |
| 310 | 2010 | myoLuc2 | GCF_000147115.1 | Arachne v. Dev. Jan 2010 | 7 | 39 | 357 | 410 | 3363 | 75, 119, GL429781:8032929-8033197 | plot myoLuc2 | |
| 311 | 2014 | nanGal1 | GCF_000622305.1 | SOAPdenovo v. 2.04.4 | 730 | 126 | 149781 | 902.5 | 980462 | 740, 12, KL200152:4088120-4089611 | plot nanGal1 | |
| 312 | 2015 | nanPar1 | GCA_000935625.1 | SOAPdenovo v. 1.06 | 1716 | 194 | 477991 | 974 | 2590489 | 552, 12, KN907832v1:31307-32422 | plot nanPar1 | |
| 313 | 2014 | nasLar1 | GCA_000772465.1 | phredPhrap v. 1.080812 | 614 | 43 | 93736 | 7 | 126885 | 117, 1, chr1:6190345-6190579 | plot nasLar1 | |
| 314 | 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 | |
| 315 | 2007 | nemVec1 | tbd | tbd | 25 | 378 | 10288 | 829 | 17106 | 769, 1, scaffold_3968:6459-7997 | plot nemVec1 | |
| 316 | 2011 | neoBri1 | GCF_000239395.1 | ALLPATHS-LG v. R36800 | 5040 | 95 | 1321574 | 20 | 665865 | 998, 20, JH422308:3325010-3327025 | plot neoBri1 | |
| 317 | 2014 | nipNip1 | GCF_000708225.1 | SOAPdenovo v. 1.6 | 41 | 154 | 11937 | 1090 | 77358 | 514, 15, KL411148:2104426-2105468 | plot nipNip1 | |
| 318 | 2010 | nomLeu1 | tbd | tbd | 859 | 141 | 220161 | 532 | 1139352 | 999, 100, GL397299:16863535-16865632 | plot nomLeu1 | |
| 319 | 2011 | nomLeu2 | tbd | tbd | 859 | 141 | 220161 | 532 | 1139352 | 999, 100, GL397299:16863535-16865632 | plot nomLeu2 | |
| 320 | 2012 | nomLeu3 | GCA_000146795.3 | tbd | 861 | 141 | 220464 | 519 | 1139552 | 999, 100, chr5:41669854-41671951 | plot nomLeu3 | |
| 321 | 2014 | notCor1 | GCF_000735185.1 | Celera Assembler v. 7.0 | 174 | 91.5 | 17942 | 51 | 21717 | 407, 1, KL665414:596304-597118 | plot notCor1 | |
| 322 | 1880 | ochPri0 | tbd | tbd | 569 | 101 | 138948 | 1065 | 1840608 | 994, 100, GeneScaffold_4726:276480-278567 | plot ochPri0 | |
| 323 | 2008 | ochPri2 | GCA_000164825.1 | tbd | 313 | 55 | 35317 | 1365 | 1110261 | 967, 100, scaffold_3914:61889-63922 | plot ochPri2 | |
| 324 | 2012 | ochPri3 | GCF_000292845.1 | Allpaths v. R41206 | 1958 | 69 | 148238 | 100 | 499781 | 890, 100, JH802177:1348834-1350713 | plot ochPri3 | |
| 325 | 2012 | octDeg1 | GCF_000260255.1 | allpaths v. R40507 LITTLE_HELPS_BIG=False | 2582 | 68 | 231489 | 100 | 464548 | 985, 100, JH651571:12809669-12811738 | plot octDeg1 | |
| 326 | 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 | |
| 327 | 2013 | oncVol1 | GCA_000499405.1 | tbd | 10 | 89.5 | 2046 | 1 | 18211 | 739, 1, HG738137v1:12037947-12039425 | plot oncVol1 | |
| 328 | 2014 | opiHoa1 | GCF_000692075.1 | SOAPdenovo v. 1.6 | 80 | 170.5 | 23360 | 1723.5 | 216549 | 855, 28, KK733898:82987-84724 | plot opiHoa1 | |
| 329 | 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 | |
| 330 | 2011 | oreNil1 | tbd | tbd | 1903 | 93 | 208888 | 20 | 734264 | 969, 20, GL831201:3474999-3476956 | plot oreNil1 | |
| 331 | 2007 | ornAna1 | GCF_000002275.2 | tbd | 793 | 49 | 70053 | 103 | 148119 | 718, 10, Contig3645:38619-40064 | plot ornAna1 | |
| 332 | 2007 | ornAna2 | GCA_000002275.2 | tbd | 793 | 49 | 70053 | 103 | 148119 | 718, 10, chrUn_DS182721v1:38619-40064 | plot ornAna2 | |
| 333 | 2012 | oryAfe1 | GCF_000298275.1 | allpaths v. R40776 LITTLE_HELPS_BIG=False | 3595 | 65 | 293465 | 100 | 691489 | 998, 100, JH863829:9451309-9453404 | plot oryAfe1 | |
| 334 | 2005 | oryCun1 | tbd | tbd | 122 | 278.5 | 44566 | 462.5 | 91832 | 978, 100, scaffold_172390:787-2842 | plot oryCun1 | |
| 335 | 2009 | oryCun2 | GCF_000003625.3 | tbd | 12 | 44.5 | 836 | 446 | 9055 | 327, 185, chr13:6520795-6521633 | plot oryCun2 | |
| 336 | 2006 | oryLat1 | tbd | tbd | 141 | 144 | 25310 | 10 | 215389 | 561, 10, chrUn:20300712-20301843 | plot oryLat1 | |
| 337 | 2005 | oryLat2 | tbd | tbd | 141 | 144 | 25310 | 10 | 253399 | 445, 10, ultracontig221:437957-438856 | plot oryLat2 | |
| 339 | 2011 | otoGar3 | GCF_000181295.1 | ALLPATHS-LG v. R35710 | 3569 | 86 | 332700 | 39 | 663694 | 985, 20, GL873641:2218538-2220527 | plot otoGar3 | |
| 340 | 2010 | oviAri1 | GCA_000005525.1 | tbd | 5934 | 53 | 394316 | 37 | 1966190 | 264, 1, chr15:8985870-8986398 | plot oviAri1 | |
| 341 | 2012 | oviAri3 | GCF_000298735.1 | SOAPdenovo v. 1.03 | 149 | 193 | 51933 | 215 | 178445 | 46, 3, chr3:3466521-3466615 | plot oviAri3 | |
| 342 | 2015 | oxyTri2 | tbd | tbd | 523 | 37 | 30028 | 50 | 25856 | 186, 1, chrMACsb310:15510646-15511018 | plot oxyTri2 | |
| 343 | 2013 | panHod1 | GCF_000400835.1 | SOAPdenovo v. 2.1 | 321 | 129 | 65178 | 1092 | 702884 | 628, 10, KE118776:1218541-1219806 | plot panHod1 | |
| 344 | 2012 | panPan1 | GCF_000258655.1 | Celera Assembler v. 5.4.3 | 63 | 133 | 11209 | 20 | 22114 | 33, 1, JH650468:842203-842269 | plot panPan1 | |
| 345 | 2015 | panPan2 | tbd | tbd | 70 | 160 | 13388 | 20 | 1045522 | 35, 1, chr4:127787143-127787213 | plot panPan2 | |
| 346 | 2013 | panRed1 | GCA_000341325.1 | Velvet v. 1.2.07 | 123 | 56 | 6626 | 10 | 3069 | 62, 10, KB454926:42673-42806 | plot panRed1 | |
| 347 | 2013 | panTig1 | GCF_000464555.1 | SOAPdenovo v. 08-Jul-2011 | 59 | 111 | 12591 | 700 | 69429 | 398, 9, KE721804:6447970-6448774 | plot panTig1 | |
| 348 | 2003 | panTro1 | tbd | tbd | 5719 | 388 | 2244063 | 100 | 3504041 | 998, 100, chr6:137473031-137475126 | plot panTro1 | |
| 349 | 2006 | panTro2 | tbd | tbd | 692 | 52 | 62006 | 240 | 238273 | 717, 10, chr10_random:5205395-5206838 | plot panTro2 | |
| 350 | 2010 | panTro3 | tbd | tbd | 472 | 54 | 44241 | 238.5 | 180280 | 908, 10, chr2B:124438762-124440587 | plot panTro3 | |
| 351 | 2011 | panTro4 | GCF_000001515.6 | tbd | 472 | 54 | 44241 | 238.5 | 180280 | 908, 10, chr2B:124438762-124440587 | plot panTro4 | |
| 352 | 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 | |
| 353 | 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 | |
| 354 | 2008 | papHam1 | tbd | tbd | 22041 | 56 | 1338445 | 50 | 2303596 | 376, 50, scaffold4259:86690-87491 | plot papHam1 | |
| 355 | 2014 | pelCri1 | GCF_000687375.1 | SOAPdenovo v. 1.6 | 3 | 72 | 517 | 186 | 808 | 386, 173, KK471910:16412-17356 | plot pelCri1 | |
| 356 | 2011 | pelSin1 | GCF_000230535.1 | SOAPdenovo v. 1.05 | 126 | 138 | 35062 | 411.5 | 167243 | 398, 10, JH212629:287260-288065 | plot pelSin1 | |
| 357 | 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 | |
| 358 | 2007 | petMar1 | tbd | tbd | 542 | 47 | 48234 | 10 | 42185 | 746, 10, Contig3178:18125-19626 | plot petMar1 | |
| 359 | 2010 | petMar2 | GCA_000148955.1 | Arachne v. 3.2 | 31 | 86 | 5681 | 732 | 39461 | 617, 100, GL479790:15647-16980 | plot petMar2 | |
| 360 | 2014 | phaCar1 | GCF_000708925.1 | SOAPdenovo v. 1.6 | 2 | 206 | 412 | 79 | 158 | 261, 100, KL416242:66648-67269 | plot phaCar1 | |
| 361 | 2014 | phaLep1 | GCF_000687285.1 | SOAPdenovo v. 1.6 | 14 | 179 | 2930 | 310 | 4227 | 343, 85, KK448216:3226-3996 | plot phaLep1 | |
| 362 | 2014 | phoRub1 | GCA_000687265.1 | SOAPdenovo v. 1.6 | 4 | 288.5 | 1016 | 195.5 | 823 | 373, 83, KK425162:48893-49721 | plot phoRub1 | |
| 363 | 2013 | phyCat1 | GCF_000472045.1 | AllPaths-LG v. January 2013 | 684 | 82.5 | 86555 | 100 | 130377 | 1000, 1, KI402232:538054-540054 | plot phyCat1 | |
| 364 | 2014 | picPub1 | GCF_000699005.1 | SOAPdenovo v. 1.6 | 59 | 83 | 12175 | 970 | 106482 | 111, 28, KL217012:74310-74559 | plot picPub1 | |
| 365 | 2013 | poeFor1 | GCF_000485575.1 | AllPaths-LG v. July 2013 | 848 | 75 | 84492 | 1 | 328834 | 972, 1, KI520524:847-2791 | plot poeFor1 | |
| 366 | 2014 | poeRet1 | tbd | tbd | 1124 | 87 | 157426 | 1 | 421252 | 988, 1, chrLG12:26078504-26080480 | plot poeRet1 | |
| 367 | 1880 | ponAbe1 | tbd | tbd | 1528 | 40 | 90824 | 133.5 | 275853 | 662, 10, Contig208:1185633-1186966 | plot ponAbe1 | |
| 368 | 2007 | ponAbe2 | tbd | tbd | 2239 | 54 | 444541 | 100 | 829820 | 769, 1, chr11:46659515-46661053 | plot ponAbe2 | |
| 369 | 2014 | priExs1 | tbd | tbd | 49 | 121 | 12100 | 1773 | 95166 | 181, 38, scaffold470:42605-43004 | plot priExs1 | |
| 370 | 2007 | priPac1 | tbd | tbd | 121 | 49 | 10688 | 209 | 31254 | 90, 1, chrUn:114913780-114913960 | plot priPac1 | |
| 372 | 2014 | priPac3 | tbd | tbd | 168 | 49.5 | 13153 | 274.5 | 50322 | 90, 1, Ppa_Contig2432:805-985 | plot priPac3 | |
| 373 | 2008 | proCap1 | GCA_000152225.1 | Arachne v. before 2009 | 116 | 38 | 5205 | 534.5 | 65619 | 53, 100, scaffold_8867:32393-32598 | plot proCap1 | |
| 374 | 2013 | pseHum1 | GCF_000331425.1 | SOAPdenovo v. 1.5 | 775 | 142 | 173055 | 10 | 547111 | 1000, 10, KB221227:5459003-5461012 | plot pseHum1 | |
| 375 | 2012 | pteAle1 | GCA_000325575.1 | SOAPdenovo v. 1.06 | 97 | 127 | 19728 | 1023 | 161616 | 421, 16, KB031157:14150143-14151000 | plot pteAle1 | |
| 376 | 2014 | pteGut1 | GCF_000699245.1 | SOAPdenovo v. 1.6 | 1 | 282 | 282 | 720 | 720 | 282, 720, KL237369:530-1813 | plot pteGut1 | |
| 377 | 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 | |
| 378 | 2008 | pteVam1 | GCA_000151845.1 | tbd | 68 | 43.5 | 9173 | 301.5 | 27212 | 971, 100, scaffold_4327:120126-122167 | plot pteVam1 | |
| 379 | 2011 | punNye1 | GCF_000239375.1 | ALLPATHS-LG v. R37016 | 1574 | 95 | 242736 | 20 | 332782 | 992, 20, JH419321:67178-69181 | plot punNye1 | |
| 380 | 2014 | pygAde1 | GCA_000699105.1 | SOAPdenovo v. 1.6 | 42 | 113 | 7740 | 1160.5 | 93198 | 78, 17, KL224983:2418932-2419104 | plot pygAde1 | |
| 381 | 2013 | pytBiv1 | GCF_000186305.1 | Soap deNovo v. March 2012 | 21222 | 101 | 2315791 | 99 | 2845128 | 649, 10, KE957835:3697-5004 | plot pytBiv1 | |
| 386 | 2005 | rheMac1 | tbd | tbd | 2816 | 39 | 116369 | 50 | 214725 | 205, 50, SCAFFOLD120616:17732-18191 | plot rheMac1 | |
| 387 | 2010 | rheMac3 | GCA_000230795.1 | SOAPdenovo v. 1.0 | 288 | 192.5 | 71777 | 1140.5 | 887215 | 949, 27, chr15:33329332-33331256 | plot rheMac3 | |
| 388 | 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 | |
| 389 | 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 | |
| 390 | 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 | |
| 391 | 2014 | rhiRox1 | GCF_000769185.1 | SOAPdenovo v. 2013.04 | 187 | 158 | 50999 | 529 | 184770 | 584, 11, KN296100v1:378785-379963 | plot rhiRox1 | |
| 392 | 1880 | ricCom1 | GCF_000151685.1 | tbd | 41 | 332 | 13808 | 738 | 38675 | 787, 3, EQ973819:99412-100988 | plot ricCom1 | |
| 393 | 2003 | rn3 | tbd | tbd | 574 | 143 | 146802 | 50 | 425043 | 72, 1, chr4:1247786-1247930 | plot rn3 | |
| 394 | 2004 | rn4 | tbd | tbd | 567 | 141 | 142452 | 50 | 424693 | 72, 1, chr4:1247786-1247930 | plot rn4 | |
| 395 | 2012 | rn5 | tbd | tbd | 64 | 516 | 32231 | 50 | 28921 | 712, 1, chr3:45275318-45276742 | plot rn5 | |
| 396 | 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 | |
| 401 | 2011 | saiBol1 | GCA_000235385.1 | AllPaths v. R37830 | 1541 | 77 | 139356 | 100 | 303093 | 1000, 100, JH378136:528784-530883 | plot saiBol1 | |
| 403 | 2011 | sarHar1 | GCF_000189315.1 | Phusion2 v. 1.0 | 17494 | 220 | 2993318 | 158 | 6574378 | 958, 10, chr1_GL834475_random:882665-884590 | plot sarHar1 | |
| 404 | 2013 | sebNig1 | GCA_000475235.1 | tbd | 168 | 55.5 | 11782 | 54.5 | 11235 | 82, 2, KI499294:4621-4786 | plot sebNig1 | |
| 405 | 2013 | sebRub1 | GCA_000475215.1 | SOAPdenovo v. 1.05 | 119 | 55 | 9711 | 51 | 8253 | 142, 1, KI444651:3586-3870 | plot sebRub1 | |
| 406 | 2014 | serCan1 | GCF_000534875.1 | tbd | 213 | 97 | 36640 | 20 | 33876 | 971, 1, HG009242:4536330-4538272 | plot serCan1 | |
| 407 | 2006 | sorAra1 | tbd | tbd | 229 | 330 | 79670 | 100 | 75086 | 895, 100, scaffold_247593:25660-27549 | plot sorAra1 | |
| 408 | 2008 | sorAra2 | GCF_000181275.1 | Allpaths v. R41070 | 3389 | 75 | 359891 | 100 | 822102 | 992, 100, JH798160:15867029-15869112 | plot sorAra2 | |
| 409 | 2008 | speTri1 | tbd | tbd | 99 | 46 | 12167 | 879 | 197520 | 835, 100, scaffold_1259:158788-160557 | plot speTri1 | |
| 410 | 2011 | speTri2 | GCF_000236235.1 | ALLPATHS v. R37591 | 2964 | 95 | 353556 | 100 | 565083 | 1000, 100, JH393486:3045059-3047158 | plot speTri2 | |
| 411 | 2014 | stePar1 | GCF_000690725.1 | ALLPATHS-LG v. August 2013 | 554 | 65 | 47063 | 1 | 120402 | 952, 1, KK580894:321554-323458 | plot stePar1 | |
| 412 | 1880 | strCam0 | tbd | tbd | 20 | 243 | 7267 | 836.5 | 40260 | 184, 13, superscaffold45:7169362-7169742 | plot strCam0 | |
| 413 | 2014 | strCam1 | GCF_000698965.1 | SOAPdenovo v. 1.6 | 19 | 246 | 7125 | 759 | 39346 | 184, 13, KL206666:4120006-4120386 | plot strCam1 | |
| 414 | 2005 | strPur1 | tbd | tbd | 1291 | 153 | 303896 | 50 | 238579 | 89, 1, Scaffold16400:576-754 | plot strPur1 | |
| 415 | 2006 | strPur2 | tbd | tbd | 367 | 55 | 25281 | 50 | 79238 | 35, 1, Scaffold12735:108654-108724 | plot strPur2 | |
| 416 | 2009 | strPur3 | tbd | tbd | 989 | 56 | 64991 | 96 | 187408 | 35, 1, Scaffold740:110486-110556 | plot strPur3 | |
| 417 | 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 | |
| 419 | 2014 | strRat2 | GCA_001040885.1 | tbd | 2 | 54.5 | 109 | 6 | 12 | 67, 1, chrUn_LN609483v1:243-377 | plot strRat2 | |
| 421 | 2009 | susScr1 | tbd | tbd | 371 | 43 | 34151 | 100 | 66500 | 986, 100, chr2:139016697-139018768 | plot susScr1 | |
| 422 | 2009 | susScr2 | tbd | tbd | 371 | 43 | 34151 | 100 | 66500 | 986, 100, chr2:139016697-139018768 | plot susScr2 | |
| 423 | 1880 | taeGut0 | tbd | tbd | 212 | 45 | 20495 | 442 | 116920 | 624, 10, Contig233:50949-52206 | plot taeGut0 | |
| 424 | 2008 | taeGut1 | tbd | tbd | 223 | 45 | 22373 | 100 | 22300 | 689, 100, chr21_random:54357-55834 | plot taeGut1 | |
| 425 | 2013 | taeGut2 | GCF_000151805.1 | PCAP v. 2008 | 219 | 44 | 21273 | 100 | 21900 | 624, 100, chr27:56676-58023 | plot taeGut2 | |
| 427 | 2013 | takFla1 | GCA_000400755.1 | HAPs v. 0.2.2 | 365 | 241 | 91817 | 788 | 407496 | 503, 1, KE121297:329-1335 | plot takFla1 | |
| 428 | 2013 | tarIhg38 | tbd | tbd | 12 | 78 | 974 | 440 | 56689 | 125, 20, chrUn_KI270442v1:175618-175887 | plot tarIhg38 | |
| 429 | 2008 | tarSyr1 | tbd | tbd | 331 | 70 | 45530 | 191 | 102767 | 892, 100, scaffold_111889:3660-5543 | plot tarSyr1 | |
| 430 | 2013 | tarSyr2 | GCF_000164805.1 | Celera v. DEC-2012 | 189 | 56 | 17645 | 20 | 9572 | 1000, 20, KE939253v1:939796-941815 | plot tarSyr2 | |
| 431 | 2014 | tauEry1 | GCF_000709365.1 | SOAPdenovo v. 1.6 | 1 | 50 | 50 | 394 | 394 | 50, 394, KL466072:20829-21322 | plot tauEry1 | |
| 432 | 2004 | tetNig1 | tbd | tbd | 64 | 272.5 | 21868 | 1000 | 53904 | 336, 59, chr5:807217-807947 | plot tetNig1 | |
| 433 | 2007 | tetNig2 | tbd | tbd | 70 | 298 | 25569 | 500 | 32404 | 336, 59, chr5:799217-799947 | plot tetNig2 | |
| 434 | 2014 | tinGut1 | GCF_000705375.1 | SOAPdenovo v. 1.6 | 18 | 96 | 3855 | 1086 | 21982 | 519, 68, KL400865:236113-237218 | plot tinGut1 | |
| 435 | 2014 | tinGut2 | GCF_000705375.1 | SOAPdenovo v. 1.6 | 18 | 96 | 3855 | 1086 | 21982 | 519, 68, KL895544:236113-237218 | plot tinGut2 | |
| 436 | 2005 | triCas1 | tbd | tbd | 75 | 100 | 8201 | 50 | 6900 | 214, 50, Contig5855_Contig1469:226794-227271 | plot triCas1 | |
| 437 | 2005 | triCas2 | tbd | tbd | 63 | 62 | 5442 | 50 | 313244 | 412, 50, chrUn_46:283716-284589 | plot triCas2 | |
| 438 | 2011 | triMan1 | GCF_000243295.1 | AllPaths v. R38542 | 5748 | 75 | 527972 | 100 | 726640 | 1000, 100, JH594622:8537918-8540017 | plot triMan1 | |
| 439 | 2011 | triSpi1 | GCF_000181795.1 | PCAP v. January 12, 2007 | 3 | 55 | 806 | 10 | 230 | 705, 10, GL622790v1:172202-173621 | plot triSpi1 | |
| 440 | 2014 | triSui1 | GCA_000701005.1 | SOAPdenovo v. 2 | 37 | 138 | 7959 | 1449 | 82883 | 120, 68, KL363219v1:83933-84240 | plot triSui1 | |
| 442 | 2013 | tupChi1 | GCF_000334495.1 | SOAPdenovo v. 1.05 | 914 | 220.5 | 290632 | 987.5 | 1823897 | 861, 16, KB320907:3306581-3308318 | plot tupChi1 | |
| 443 | 2008 | turTru1 | tbd | tbd | 112 | 41.5 | 15556 | 388 | 52461 | 993, 100, scaffold_108458:6669-8754 | plot turTru1 | |
| 444 | 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 | |
| 445 | 2014 | tytAlb1 | GCF_000687205.1 | SOAPdenovo v. 1.6 | 2 | 170 | 340 | 326 | 652 | 289, 220, KK379918:2163-2960 | plot tytAlb1 | |
| 446 | 2014 | ursMar1 | GCF_000687225.1 | SOAPdenovo v. 1.05 | 205 | 41 | 12130 | 3384 | 708704 | 711, 49, KK498595:3401141-3402611 | plot ursMar1 | |
| 447 | 2007 | venter1 | tbd | tbd | 64 | 411.5 | 26995 | 100 | 64592 | 862, 20, chr2:102870978-102872721 | plot venter1 | |
| 448 | 2008 | vicPac1 | tbd | tbd | 221 | 251 | 71912 | 276 | 310711 | 993, 100, scaffold_812:411693-413778 | plot vicPac1 | |
| 449 | 2013 | vicPac2 | GCF_000164845.1 | Newbler v. May-2012 | 1245 | 69 | 115488 | 369 | 430947 | 685, 20, KB632527:971889-973278 | plot vicPac2 | |
| 450 | 1880 | vicVic1 | tbd | tbd | 218 | 252.5 | 71401 | 263 | 309237 | 993, 100, scaffold_812:411693-413778 | plot vicVic1 | |
| 451 | 2016 | xenLae2 | GCF_001663975.1 | Meraculous v. May-2013 | 2660 | 43 | 112843 | 265 | 1906995 | 50, 10, chr6S:105116072-105116181 | plot xenLae2 | |
| 452 | 2004 | xenTro1 | tbd | tbd | 140 | 177.5 | 37717 | 889.5 | 437093 | 94, 1, scaffold_26179:153-341 | plot xenTro1 | |
| 453 | 2005 | xenTro2 | tbd | tbd | 116 | 229.5 | 33928 | 806.5 | 320973 | 83, 1, scaffold_13788:6263-6429 | plot xenTro2 | |
| 454 | 2009 | xenTro3 | tbd | tbd | 116 | 229.5 | 33928 | 806.5 | 320973 | 83, 1, GL185958:6263-6429 | plot xenTro3 | |
| 455 | 2012 | xenTro7 | GCF_000004195.2 | ARACHNE v. 20071016_modified | 98 | 82.5 | 16149 | 201 | 69741 | 775, 100, KB022861:7377-9026 | plot xenTro7 | |
| 456 | 2016 | xenTro9 | GCF_000004195.3 | Meraculous v. May-2013 | 172 | 105.5 | 27368 | 100 | 99243 | 775, 100, chrUn_NW_016684502v1:7377-9026 | plot xenTro9 | |
| 457 | 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 | |
| 459 | 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 | 2006 | borEut13 | tbd | 0 | tbd |
| 005 | 2014 | bunEbo1 | GCF_000889155.1 | 0 | tbd |
| 006 | 2010 | caeJap3 | tbd | 0 | tbd |
| 007 | 2003 | canFamPoodle1 | GCA_000181415.1 | 0 | tbd |
| 008 | 2005 | canHg12 | tbd | 0 | tbd |
| 009 | 2010 | ce10 | tbd | 0 | tbd |
| 010 | 2013 | ce11 | GCF_000002985.6 | 0 | tbd |
| 011 | 2004 | ce2 | tbd | 5 | tbd |
| 012 | 2005 | ce3 | tbd | 0 | tbd |
| 013 | 2007 | ce4 | tbd | 0 | tbd |
| 014 | 2007 | ce5 | tbd | 0 | tbd |
| 015 | 2008 | ce6 | tbd | 0 | tbd |
| 016 | 2009 | ce7 | tbd | 0 | tbd |
| 017 | 2009 | ce8 | tbd | 0 | tbd |
| 018 | 2010 | ce9 | tbd | 0 | tbd |
| 019 | 2004 | droMoj1 | tbd | 0 | tbd |
| 020 | 2014 | eboVir1 | tbd | 2 | tbd |
| 021 | 2014 | eboVir3 | tbd | 0 | tbd |
| 022 | 2006 | euaGli13 | tbd | 19510 | tbd |
| 023 | 2006 | eutHer13 | tbd | 304 | tbd |
| 024 | 1880 | gasAsc0 | GCA_000180675.1 | 0 | tbd |
| 025 | 2006 | gliRes13 | tbd | 39623 | tbd |
| 026 | 2016 | gorGor5 | tbd | 0 | tbd |
| 027 | 2006 | homIni14 | tbd | 0 | tbd |
| 028 | 1880 | homNea0 | tbd | 872 | tbd |
| 029 | 2006 | lauRas13 | tbd | 31794 | tbd |
| 030 | 2014 | marVir1 | tbd | 0 | tbd |
| 031 | 2008 | melHap1 | GCA_000172435.1 | 0 | tbd |
| 032 | 2008 | melInc1 | GCA_000180415.1 | 0 | tbd |
| 033 | 2006 | otoGar1 | tbd | 0 | tbd |
| 034 | 2008 | priPac2 | GCA_000180635.1 | 59 | tbd |
| 035 | 2012 | repBase0 | tbd | 2137 | tbd |
| 036 | 2012 | repBase1 | tbd | 3623 | tbd |
| 037 | 1880 | repBase2 | tbd | 3237 | tbd |
| 038 | 2014 | resEbo1 | GCF_000854085.1 | 0 | tbd |
| 039 | 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 |
| 040 | 2003 | sacCer1 | tbd | 0 | tbd |
| 041 | 2008 | sacCer2 | tbd | 0 | tbd |
| 042 | 2011 | sacCer3 | GCF_000146045.2 | 0 | tbd |
| 043 | 1880 | salMan0 | tbd | 0 | tbd |
| 044 | 2011 | strRat1 | tbd | 3207 | tbd |
| 045 | 2014 | sudEbo1 | GCF_000855585.1 | 0 | tbd |
| 046 | 2014 | taiEbo1 | GCF_000888475.1 | 0 | tbd |
| 047 | 2006 | tupBel1 | tbd | 0 | tbd |
| 048 | 2014 | zaiEbo1 | GCF_000848505.1 | 0 | tbd |
