Hg38 100-way Genome size statistics: Difference between revisions

Revision as of 18:21, 13 February 2015

statistics collected from UCSC 2bit files

The external link in the first column goes to the FTP location where the genome sequence was obtained
The external links from the UCSC database name go to the UCSC genome-test browser for that genome
N bases == unknown bases in the assembly marked by "N"
non-N bases == called bases in the assembly
total size == all bases in assembly, N and non-N
The % masked is masking from Repeat Masker or Window Masker plus TRF/Simple Repeats, whichever is greater, usually WindowMasker for these genomes
The common name external links go to information pages for this genome
The coverage numbers are taken directly from information README files from the sequencing center
The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser

do not edit, automatically generated table

order count/ ftp src	ucsc db name/ genome-test	chrom count	total size	non-N bases	N base count	% masked	common name/ src info	coverage	N50 chrom.sizes	alignment type	% of hg38 matched (chainLink table)	chain minScore	chain linearGap
01	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	N/A	N/A	3000	medium
02	panTro4	24,129	3,309,577,922	2,902,338,967	407,238,955	% 51.29	Chimp	6X	143986469	Net	93.112%	5000	medium
03	gorGor3	46,823	3,029,553,646	2,822,760,080	206,793,566	% 48.80	Gorilla	2.1X	145327772	Net	88.005%	3000	medium
04	ponAbe2	55	3,446,771,396	3,093,543,172	353,228,224	% 50.89	Orangutan	6X	135191526	Net	89.187%	5000	medium
05	nomLeu3	17,492	2,962,077,449	2,756,609,047	205,468,402	% 51.14	Gibbon	5.6X	117381234	Net	86.379%	3000	medium
06	macFas5	7,601	2,946,843,737	2,803,866,385	142,977,352	% 50.11	Crab-eating macaque	68X	152835861	Net	85.675%	3000	medium
07	rheMac3	34,103	2,969,988,180	2,639,145,830	330,842,350	% 48.54	Rhesus	50X	150158102	Net	79.729%	5000	medium
08	papAnu2	63,250	2,948,380,710	2,893,250,291	55,130,419	% 38.95	Baboon	85X	139646187	Net	84.179%	3000	medium
09	saiBol1	2,685	2,608,572,064	2,477,131,095	131,440,969	% 46.69	Squirrel monkey	80X	18744880	Net	70.565%	3000	medium
10	chlSab2	2,004	2,789,656,328	2,752,000,999	37,655,329	% 48.77	Green monkey	95X	101219884	Net	84.393%	5000	medium
11	calJac3	14,205	2,914,958,544	2,752,505,800	162,452,744	% 47.71	Marmoset	6X	132174527	Net	71.709%	3000	medium
12	oryAfe1	22,509	4,444,080,527	3,415,340,621	1,028,739,906	% 31.09	Aardvark	44X	7875832	Net	36.526%	3000	medium
13	otoGar3	7,793	2,519,724,550	2,359,530,453	160,194,097	% 39.51	Bushbaby	137X	13852661	Net	49.485%	3000	medium
14	cerSim1	3,087	2,464,367,180	2,366,858,012	97,509,168	% 38.80	White rhinoceros	91X	26277727	Net	53.075%	3000	medium
15	chrAsi1	20,500	4,210,110,458	3,363,564,316	846,546,142	% 20.11	Cape golden mole	66X	13470186	Net	29.208%	3000	medium
16	eptFus1	6,788	2,026,627,185	1,811,378,799	215,248,386	% 24.11	Big brown bat	84X	13454942	Net	36.386%	3000	medium
17	tupChi1	50,750	2,846,580,235	2,706,389,135	140,191,100	% 40.02	Chinese tree shrew	80X	3670124	Net	37.022%	3000	medium
18	equCab2	34	2,484,532,062	2,428,790,173	55,741,889	% 40.97	Horse	6.8X	91571448	Net	52.083%	3000	medium
19	camFer1	13,334	2,009,194,609	1,985,416,433	23,778,176	% 33.32	Bactrian camel	30X	2005940	Net	46.206%	3000	medium
20	vicPac2	276,611	2,172,177,994	2,078,582,856	93,595,138	% 35.40	Alpaca	22X	7263804	Net	45.887%	3000	medium
21	turTru2	240,901	2,551,996,573	2,332,402,443	219,594,130	% 43.56	Dolphin	3.5X	116261	Net	46.072%	3000	medium
22	canFam3	3,268	2,410,976,875	2,392,715,236	18,261,639	% 43.01	Dog	7.6X	63241923	Net	49.978%	3000	medium
23	orcOrc1	1,668	2,372,919,877	2,249,582,112	123,337,765	% 42.47	Killer whale	200X	12735091	Net	47.281%	3000	medium
24	speTri2	12,483	2,478,393,770	2,311,060,300	167,333,470	% 36.27	Squirrel	495X	8192786	Net	44.729%	3000	medium
25	pteAle1	65,597	1,985,958,707	1,944,625,202	41,333,505	% 32.56	Black flying-fox	110X	15954802	Net	45.612%	3000	medium
26	susScr3	4,583	2,808,525,991	2,518,987,191	289,538,800	% 44.30	Pig	24X	148491826	Net	41.326%	3000	medium
27	loxAfr3	2,353	3,196,760,833	3,118,565,340	78,195,493	% 47.63	Elephant	7X	46401353	Net	41.904%	3000	medium
28	hetGla2	4,229	2,618,204,639	2,314,771,103	303,433,536	% 32.31	Naked mole-rat	90X	20532749	Net	42.315%	3000	medium
29	pteVam1	96,944	1,996,076,410	1,839,436,660	156,639,750	% 31.75	Megabat	2X	124060	Net	41.012%	3000	medium
30	felCat8	267,625	2,641,342,258	2,599,700,169	41,642,089	% 44.41	Cat	20X	142431058	Net	47.700%	3000	medium
31	ailMel1	81,467	2,299,509,015	2,245,312,831	54,196,184	% 38.96	Panda	73X	1281781	Net	48.226%	3000	medium
32	musFur1	7,741	2,410,758,013	2,277,906,570	132,851,443	% 38.98	Ferret	162X	9335154	Net	45.782%	3000	medium
33	cavPor3	3,144	2,723,219,641	2,663,369,733	59,849,908	% 27.53	Guinea pig	6.76X	27942054	Net	37.901%	3000	medium
34	dasNov3	46,559	3,631,522,711	3,299,882,028	331,640,683	% 49.28	Armadillo	6X	1687935	Net	42.233%	3000	medium
35	oryCun2	3,242	2,737,490,501	2,604,023,284	133,467,217	% 43.74	Rabbit	6.51X	111795807	Net	38.631%	3000	medium
36	panHod1	15,059	2,696,886,330	2,507,986,438	188,899,892	% 42.51	Tibetan antelope	67X	2772860	Net	41.357%	3000	medium
37	lepWed1	16,711	3,156,902,762	2,223,164,129	933,738,633	% 40.09	Weddell seal	82X	904031	Net	47.437%	3000	medium
38	odoRosDiv1	3,892	2,400,133,628	2,300,235,509	99,898,119	% 40.52	Pacific walrus	200X	2616778	Net	47.985%	3000	medium
39	myoDav1	101,769	2,059,799,708	1,878,461,987	181,337,721	% 23.35	David's myotis (bat)	110X	3454484	Net	34.892%	3000	medium
40	bosTau8	3,179	2,670,044,500	2,649,304,231	20,740,269	% 48.69	Cow	9X	105708250	Net	45.975%	3000	medium
41	capHir1	77,021	2,635,848,900	2,495,939,845	139,909,055	% 43.55	Domestic goat	86.64X	92306894	Net	N/A	3000	medium
42	oviAri3	5,698	2,619,054,388	2,534,335,866	84,718,522	% 45.18	Sheep	142X	100079507	Net	41.193%	3000	medium
43	myoLuc2	11,654	2,034,575,300	1,966,419,868	68,155,432	% 33.71	Microbat	2.18X	4293315	Net	35.148%	3000	medium
44	eleEdw1	8,768	3,843,982,861	3,315,871,847	528,111,014	% 49.11	Cape elephant shrew	62X	15011382	Net	22.161%	3000	medium
45	triMan1	6,323	3,103,808,406	2,769,099,677	334,708,729	% 36.24	Manatee	150X	14442683	Net	41.443%	3000	medium
46	jacJac1	10,896	2,835,242,767	2,470,259,869	364,982,898	% 37.29	Lesser Egyptian jerboa	78X	22080993	Net	27.899%	3000	medium
47	chiLan1	2,838	2,390,852,391	2,284,276,400	106,575,991	% 30.82	Chinchilla	87X	21893125	Net	40.808%	3000	medium
48	conCri1	2,038	1,769,657,897	1,682,542,007	87,115,890	% 18.21	Star-nosed mole	113.1X	55520359	Net	33.037%	3000	medium
49	octDeg1	7,134	2,995,882,938	2,526,254,692	469,628,246	% 26.47	Brush-tailed rat	80X	12091372	Net	35.827%	3000	medium
50	ochPri3	10,420	2,229,835,716	1,943,987,870	285,847,846	% 29.53	Pika	103X	26863993	Net	30.261%	3000	medium
51	eriEur2	5,803	2,715,720,925	2,333,073,535	382,647,390	% 45.60	Hedgehog	79X	3264618	Net	21.643%	3000	medium
52	echTel2	8,402	2,947,024,286	2,605,196,361	341,827,925	% 28.26	Tenrec	78X	45764842	Net	27.550%	3000	medium
53	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	Net	31.629%	3000	medium
54	rn6	953	2,870,182,909	2,729,860,805	140,322,104	% 43.31	Rat	10X	145729302	Net	N/A	1000	N/A
55	criGri1	52,711	2,360,146,428	2,301,325,917	58,820,511	% 27.06	Chinese hamster	130X	1558295	Net	N/A	1000	N/A
56	mesAur1	21,484	2,504,925,039	2,076,176,254	428,748,785	% 25.70	Golden hamster	115X	12753307	Net	N/A	1000	N/A
57	micOch1	6,335	2,287,340,943	2,104,321,675	183,019,268	% 23.89	Prairie vole	94X	61813736	Net	N/A	1000	N/A
58	sorAra2	12,845	2,423,158,183	2,192,103,426	231,054,757	% 32.76	Shrew	120X	22794405	Net	N/A	1000	N/A
59	macEug2	277,711	3,075,184,024	2,536,076,954	539,107,070	% 47.39	Wallaby	2X	36602	Net	N/A	1000	N/A
60	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	Net	14.370%	5000	loose
61	sarHar1	35,974	3,174,693,010	2,931,539,702	243,153,308	% 39.66	Tasmanian devil	85X	1847106	Net	N/A	1000	N/A
62	apaSpi1	286,620	1,931,078,847	1,877,982,184	53,096,663	% 29.87	Spiny softshell turtle	33.4X	2306994	Net	N/A	1000	N/A
63	cheMyd1	140,023	2,208,410,377	2,110,381,997	98,028,380	% 29.65	Green seaturtle	110X	3864108	Net	6.296%	5000	loose
64	chrPic2	78,595	2,365,766,562	2,173,204,089	192,562,473	% 31.52	Painted turtle	15X	7072151	Net	6.708%	5000	loose
65	pelSin1	19,904	2,202,483,752	2,106,639,384	95,844,368	% 33.82	Chinese softshell turtle	105X	3350749	Net	N/A	1000	N/A
66	ornAna1	201,523	1,996,811,212	1,842,235,522	154,575,690	% 47.89	Platypus	6X	991605	Net	N/A	1000	N/A
67	allMis1	14,645	2,174,259,888	2,128,720,123	45,539,765	% 37.18	American alligator	68X	508966	Net	N/A	1000	N/A
68	colLiv1	14,923	1,107,989,085	1,086,925,875	21,063,210	% 19.83	Rock pigeon	60X	3148738	Net	N/A	1000	N/A
69	galGal4	15,932	1,046,932,099	1,032,854,810	14,077,289	% 20.41	Chicken	12X	90216835	Net	N/A	1000	N/A
70	anoCar2	6,457	1,799,143,587	1,701,353,767	97,789,820	% 41.98	Lizard	7.1X	150641573	Net	3.593%	5000	loose
71	anaPla1	78,488	1,105,052,351	1,069,972,754	35,079,597	% 20.21	Mallard duck	60X	1233631	Net	N/A	1000	N/A
72	melGal1	5,891	1,061,817,101	935,922,386	125,894,715	% 6.60	Turkey	5X	74864452	Net	N/A	1000	N/A
73	falChe1	5,863	1,174,811,715	1,150,993,769	23,817,946	% 18.62	Saker falcon	147X	4154532	Net	N/A	1000	N/A
74	falPer1	7,021	1,171,973,431	1,153,404,348	18,569,083	% 18.69	Peregrine falcon	137.6X	3935757	Net	N/A	1000	N/A
75	amaVit1	182,974	1,175,404,042	1,128,255,752	47,148,290	% 18.36	Parrot	24X	19239	Net	N/A	1000	N/A
76	araMac1	192,790	1,204,700,227	997,522,769	207,177,458	% 16.49	Scarlet Macaw	26X	15974	Net	N/A	1000	N/A
77	pseHum1	5,406	1,042,997,632	1,030,030,436	12,967,196	% 20.21	Tibetan ground jay	96.25X	16337386	Net	N/A	1000	N/A
78	melUnd1	25,212	1,117,373,619	1,086,614,815	30,758,804	% 19.62	Budgerigar	7X	10614383	Net	N/A	1000	N/A
79	ficAlb2	21,428	1,118,343,587	1,102,323,882	16,019,705	% 24.04	Collared flycatcher	60X	64724594	Net	N/A	1000	N/A
80	zonAlb1	6,018	1,052,600,561	1,006,293,510	46,307,051	% 20.03	White-throated sparrow	63X	4866725	Net	N/A	1000	N/A
81	geoFor1	27,239	1,065,292,181	1,041,286,029	24,006,152	% 19.99	Medium ground finch	115X	5255844	Net	N/A	1000	N/A
82	taeGut2	37,096	1,232,135,591	1,222,864,691	9,270,900	% 8.11	Zebra finch	5.5X	62374962	Net	N/A	1000	N/A
83	lepOcu1	1,925	945,874,548	869,414,359	76,460,189	% 24.85	Spotted gar	677.5X	50348508	Net	N/A	1000	N/A
84	xenTro7	7,728	1,437,530,879	1,365,936,747	71,594,132	% 33.98	X. tropicalis	7.44X	124127367	Net	N/A	1000	N/A
85	latCha1	22,819	2,860,591,921	2,183,592,768	676,999,153	% 45.68	Coelacanth	77.5X	924513	Net	N/A	1000	N/A
86	gadMor1	427,428	824,327,835	608,038,555	216,289,280	% 31.25	Atlantic cod	40X	393166	Net	N/A	1000	N/A
87	gasAcu1	23	463,354,448	446,627,861	16,726,587	% 2.58	Stickleback	6X	20083130	Net	N/A	1000	N/A
88	oreNil2	5,678	927,696,114	816,084,674	111,611,440	% 25.51	Nile tilapia	269X	27159252	Net	N/A	1000	N/A
89	tetNig2	27	358,618,246	302,314,788	56,303,458	% 20.27	Tetraodon	7.9X	13390619	Net	N/A	1000	N/A
90	neoBri1	9,083	847,883,811	685,897,279	161,986,532	% 24.12	Princess of Burundi	171X	4430025	Net	N/A	1000	N/A
91	takFla1	34,223	377,992,166	314,409,984	63,582,182	% 17.77	Yellowbelly pufferfish	131X	315240	Net	N/A	1000	N/A
92	hapBur1	7,994	831,398,301	698,936,397	132,461,904	% 24.10	Burton's mouthbreeder	131X	1194190	Net	N/A	1000	N/A
93	fr3	6,835	391,484,715	350,961,831	40,522,884	% 19.01	Fugu	8.5X	11516971	Net	N/A	1000	N/A
94	astMex1	10,736	1,191,259,254	964,251,514	227,007,740	% 39.11	Mexican tetra (cavefish)	70X	1775308	Net	N/A	1000	N/A
95	petMar2	25,006	885,550,958	647,368,134	238,182,824	% 42.47	Lamprey	5.0X	184619	Net	1.265%	5000	loose
96	danRer10	1,061	1,371,719,383	1,369,631,918	2,087,465	% 52.32	Zebrafish	30X	53345113	Net	3.357%	5000	loose
97	mayZeb1	3,725	849,595,388	713,527,863	136,067,525	% 25.04	Zebra Mbuna	129.7X	3702874	Net	1.805%	5000	loose
98	punNye1	7,233	830,129,318	698,757,151	131,372,167	% 24.56	Pundamilia nyererei	126X	2525540	Net	1.787%	5000	loose
99	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	Net	2.002%	5000	loose
100	xipMac1	20,632	729,664,433	652,811,251	76,853,182	% 26.62	Southern platyfish	19.6X	1303070	Net	1.898%	5000	loose

@@ Line 405: / Line 405: @@
 <TH ALIGN=CENTER>92306894</TH>
    <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>N/A</TD>
-<TD ALIGN=RIGHT>1000</TD>
+<TD ALIGN=RIGHT>3000</TD>
-   <TD ALIGN=CENTER>N/A</TD></TR>
+   <TD ALIGN=CENTER>medium</TD></TR>
 <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000298735.1/ 42]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oviAri3 oviAri3]</TH>
 <TH ALIGN=RIGHT>5,698</TH>
@@ Line 431: / Line 431: @@
    <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Elephantulus_edwardii/EleEdw1.0/ Cape elephant shrew]</TD><TH ALIGN=CENTER>62X</TH>
 <TH ALIGN=CENTER>15011382</TH>
-   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>N/A</TD>
+   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>22.161%</TD>
-<TD ALIGN=RIGHT>1000</TD>
+<TD ALIGN=RIGHT>3000</TD>
-   <TD ALIGN=CENTER>N/A</TD></TR>
+   <TD ALIGN=CENTER>medium</TD></TR>
 <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/10467 45]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 triMan1]</TH>
 <TH ALIGN=RIGHT>6,323</TH>
@@ Line 440: / Line 440: @@
    <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHIN01 Manatee]</TD><TH ALIGN=CENTER>150X</TH>
 <TH ALIGN=CENTER>14442683</TH>
-   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>N/A</TD>
+   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>41.443%</TD>
-<TD ALIGN=RIGHT>1000</TD>
+<TD ALIGN=RIGHT>3000</TD>
-   <TD ALIGN=CENTER>N/A</TD></TR>
+   <TD ALIGN=CENTER>medium</TD></TR>
 <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000280705.1/ 46]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=jacJac1 jacJac1]</TH>
 <TH ALIGN=RIGHT>10,896</TH>
@@ Line 467: / Line 467: @@
    <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Condylura_cristata/ConCri1.0/ Star-nosed mole]</TD><TH ALIGN=CENTER>113.1X</TH>
 <TH ALIGN=CENTER>55520359</TH>
-   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>N/A</TD>
+   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>33.037%</TD>
-<TD ALIGN=RIGHT>1000</TD>
+<TD ALIGN=RIGHT>3000</TD>
-   <TD ALIGN=CENTER>N/A</TD></TR>
+   <TD ALIGN=CENTER>medium</TD></TR>
 <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000260255.1/ 49]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=octDeg1 octDeg1]</TH>
 <TH ALIGN=RIGHT>7,134</TH>
@@ Line 485: / Line 485: @@
    <TD ALIGN=CENTER>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ochotona_princeps/OchPri3.0/ Pika]</TD><TH ALIGN=CENTER>103X</TH>
 <TH ALIGN=CENTER>26863993</TH>
-   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>N/A</TD>
+   <TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>30.261%</TD>
-<TD ALIGN=RIGHT>1000</TD>
+<TD ALIGN=RIGHT>3000</TD>
-   <TD ALIGN=CENTER>N/A</TD></TR>
+   <TD ALIGN=CENTER>medium</TD></TR>
 <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000296755.1/ 51]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur2 eriEur2]</TH>
 <TH ALIGN=RIGHT>5,803</TH>

Hg38 100-way Genome size statistics: Difference between revisions

Revision as of 18:21, 13 February 2015

see also

statistics collected from UCSC 2bit files

do not edit, automatically generated table

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