Hg19 100way Genome size statistics

see also

• Human 100-way Hg19 100way conservation alignment
• Human 100-way Hg19 100way conservation lastz parameters
• all other UCSC Multiple Alignments

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 hg19 matched (chainLink table)	chain minScore	chain linearGap
01	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	N/A	N/A	N/A	N/A
02	panTro4	24,129	3,309,577,922	2,902,338,967	407,238,955	% 51.29	Chimp	6X	143986469	RecipBest	95.279%	5000	medium
03	gorGor3	46,823	3,029,553,646	2,822,760,080	206,793,566	% 48.80	Gorilla	2.1X	145327772	SyntenicNet	89.876%	5000	medium
04	ponAbe2	55	3,446,771,396	3,093,543,172	353,228,224	% 50.89	Orangutan	6X	135191526	SyntenicNet	91.350%	5000	medium
05	nomLeu3	17,492	2,962,077,449	2,756,609,047	205,468,402	% 51.14	Gibbon		117381234	SyntenicNet	87.764%	5000	medium
06	chlSab1	2,004	2,789,656,328	2,752,000,999	37,655,329	% 48.77	Chlorocebus sabaeus		101219884	RecipBest	86.446%	5000	medium
07	macFas5	7,601	2,946,843,737	2,803,866,385	142,977,352	% 50.11	Macaca fascicularis		152835861	RecipBest	86.666%	5000	medium
08	rheMac3	34,103	2,969,988,180	2,639,145,830	330,842,350	% 48.54	Rhesus	50X	150158102	SyntenicNet	82.859%	5000	medium
09	papHam1	387,374	2,867,564,654	2,741,849,051	125,715,603	% 48.70	Baboon	5.3X	88525	RecipBest	82.810%	5000	medium
10	saiBol1	2,685	2,608,572,064	2,477,131,095	131,440,969	% 46.69	Squirrel monkey	80X	18744880	RecipBest	69.598%	5000	medium
11	calJac3	14,205	2,914,958,544	2,752,505,800	162,452,744	% 47.71	Marmoset	6X	132174527	SyntenicNet	70.654%	5000	medium
12	otoGar3	7,793	2,519,724,550	2,359,530,453	160,194,097	% 39.51	Bushbaby	137X	13852661	RecipBest	54.830%	3000	medium
13	tupChi1	50,750	2,846,580,235	2,706,389,135	140,191,100	% 40.02	Tupaia chinensis		3670124	RecipBest	46.558%	3000	medium
14	cerSim1	3,087	2,464,367,180	2,366,858,012	97,509,168	% 38.80	White rhinoceros		26277727	Net	58.103%	3000	medium
15	equCab2	34	2,484,532,062	2,428,790,173	55,741,889	% 40.97	Horse	6.8X	91571448	SyntenicNet	57.050%	3000	medium
16	camFer1	13,334	2,009,194,609	1,985,416,433	23,778,176	% 33.32	Camelus ferus		2005940	RecipBest	50.419%	3000	medium
17	vicPac2	276,611	2,172,177,994	2,078,582,856	93,595,138	% 35.40	Alpaca		7263804	RecipBest	50.193%	3000	medium
18	orcOrc1	1,668	2,372,919,877	2,249,582,112	123,337,765	% 42.47	Orcinus orca		12735091	N/A	N/A	1000	N/A
19	turTru2	240,901	2,551,996,573	2,332,402,443	219,594,130	% 43.56	Dolphin	3.5X	116261	N/A	N/A	1000	N/A
20	musFur1	7,741	2,410,758,013	2,277,906,570	132,851,443	% 38.98	Ferret		9335154	RecipBest	50.993%	3000	medium
21	oryAfe1	22,509	4,444,080,527	3,415,340,621	1,028,739,906	% 31.09	Orycteropus afer		7875832	RecipBest	41.668%	3000	medium
22	speTri2	12,483	2,478,393,770	2,311,060,300	167,333,470	% 36.27	Squirrel	495X	8192786	N/A	N/A	1000	N/A
23	pteAle1	65,597	1,985,958,707	1,944,625,202	41,333,505	% 32.56	Pteropus alecto		15954802	N/A	N/A	1000	N/A
24	susScr3	4,583	2,808,525,991	2,518,987,191	289,538,800	% 44.30	Pig	24X	148491826	N/A	N/A	1000	N/A
25	triMan1	6,323	3,103,808,406	2,769,099,677	334,708,729	% 36.24	Manatee	150X	14442683	RecipBest	46.580%	3000	medium
26	octDeg1	7,134	2,995,882,938	2,526,254,692	469,628,246	% 26.47	Octodon degus		12091372	RecipBest	41.385%	3000	medium
27	pteVam1	96,944	1,996,076,410	1,839,436,660	156,639,750	% 31.75	Megabat	2X	124060	RecipBest	45.414%	3000	medium
28	loxAfr3	2,353	3,196,760,833	3,118,565,340	78,195,493	% 47.63	Elephant	7X	46401353	SyntenicNet	46.636%	3000	medium
29	felCat5	5,500	2,455,541,136	2,364,296,207	91,244,929	% 43.24	Cat	12X	148491654	RecipBest	52.426%	3000	medium
30	ailMel1	81,467	2,299,509,015	2,245,312,831	54,196,184	% 38.96	Panda	73X	1281781	SyntenicNet	50.022%	3000	medium
31	canFam3	3,268	2,410,976,875	2,392,715,236	18,261,639	% 43.01	Dog	7.6X	63241923	SyntenicNet	51.848%	3000	medium
32	chrAsi1	20,500	4,210,110,458	3,363,564,316	846,546,142	% 20.11	Chrysochloris asiatica		13470186	RecipBest	34.209%	3000	medium
33	dasNov3	46,559	3,631,522,711	3,299,882,028	331,640,683	% 49.28	Armadillo	6X	1687935	RecipBest	46.571%	3000	medium
34	oryCun2	3,242	2,737,490,501	2,604,023,284	133,467,217	% 43.74	Rabbit	6.51X	111795807	SyntenicNet	44.317%	3000	medium
35	myoDav1	101,769	2,059,799,708	1,878,461,987	181,337,721	% 23.35	Myotis Davidii		3454484	N/A	N/A	1000	N/A
36	panHod1	15,059	2,696,886,330	2,507,986,438	188,899,892	% 42.51	Pantholops hodgsonii		2772860	SyntenicNet	46.863%	3000	medium
37	lepWed1	16,711	3,156,902,762	2,223,164,129	933,738,633	% 40.09	Leptonychotes weddellii		904031	RecipBest	52.424%	3000	medium
38	odoRosDiv1	3,892	2,400,133,628	2,300,235,509	99,898,119	% 40.52	Odobenus rosmarus divergens		2616778	RecipBest	53.559%	3000	medium
39	myoLuc2	11,654	2,034,575,300	1,966,419,868	68,155,432	% 33.71	Microbat	2.18X	4293315	N/A	N/A	1000	N/A
40	eptFus1	6,788	2,026,627,185	1,811,378,799	215,248,386	% 24.11	Eptesicus fuscus		13454942	N/A	N/A	1000	N/A
41	bosTau7	11,692	2,981,119,579	2,804,673,174	176,446,405	% 49.56	Cow	7.1X	85119472	SyntenicNet	46.971%	3000	medium
42	capHir1	77,021	2,635,848,900	2,495,939,845	139,909,055	% 43.55	Capra hircus		92306894	SyntenicNet	46.498%	3000	medium
43	oviAri3	5,698	2,619,054,388	2,534,335,866	84,718,522	% 45.18	Sheep		100079507	RecipBest	46.833%	3000	medium
44	hetGla2	4,229	2,618,204,639	2,314,771,103	303,433,536	% 32.31	Naked mole-rat	90X	20532749	SyntenicNet	47.600%	3000	medium
45	eleEdw1	8,768	3,843,982,861	3,315,871,847	528,111,014	% 49.11	Elephantulus edwardii		15011382	RecipBest	27.675%	3000	medium
46	jacJac1	10,896	2,835,242,767	2,470,259,869	364,982,898	% 37.29	Jaculus jaculus		22080993	RecipBest	35.106%	3000	medium
47	chiLan1	2,838	2,390,852,391	2,284,276,400	106,575,991	% 30.82	Chinchilla		21893125	N/A	N/A	1000	N/A
48	cavPor3	3,144	2,723,219,641	2,663,369,733	59,849,908	% 27.53	Guinea pig	6.76X	27942054	SyntenicNet	43.680%	3000	medium
49	conCri1	2,038	1,769,657,897	1,682,542,007	87,115,890	% 18.21	Condylura cristata		55520359	RecipBest	37.034%	3000	medium
50	ochPri3	10,420	2,229,835,716	1,943,987,870	285,847,846	% 29.53	Pika		26863993	RecipBest	34.676%	3000	medium
51	eriEur2	5,803	2,715,720,925	2,333,073,535	382,647,390	% 45.60	Hedgehog		3264618	RecipBest	26.149%	3000	medium
52	echTel2	8,402	2,947,024,286	2,605,196,361	341,827,925	% 28.26	Tenrec		45764842	RecipBest	30.135%	3000	medium
53	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	RecipBest	35.249%	3000	medium
54	rn5	2,739	2,909,698,938	2,572,853,723	336,845,215	% 42.81	Rat	6X	154597545	SyntenicNet	31.662%	3000	medium
55	criGri1	52,711	2,360,146,428	2,301,325,917	58,820,511	% 26.43	Cricetulus griseus		1558295	N/A	N/A	1000	N/A
56	mesAur1	21,484	2,504,925,039	2,076,176,254	428,748,785	% 25.70	Mesocricetus auratus		12753307	N/A	N/A	1000	N/A
57	micOch1	6,335	2,287,340,943	2,104,321,675	183,019,268	% 23.89	Microtus ochrogaster		61813736	N/A	N/A	1000	N/A
58	sorAra2	12,845	2,423,158,183	2,192,103,426	231,054,757	% 32.76	Shrew		22794405	RecipBest	27.681%	3000	medium
59	macEug2	277,711	3,075,184,024	2,536,076,954	539,107,070	% 47.39	Wallaby	2X	36602	RecipBest	6.534%	5000	loose
60	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	SyntenicNet	14.358%	5000	loose
61	cheMyd1	140,023	2,208,410,377	2,110,381,997	98,028,380	% 29.65	Chelonia mydas		3864108	N/A	N/A	1000	N/A
62	sarHar1	35,974	3,174,693,010	2,931,539,702	243,153,308	% 39.66	Tasmanian devil	85X	1847106	RecipBest	7.414%	5000	loose
63	chrPic1	80,984	2,589,745,704	2,158,289,746	431,455,958	% 31.20	Painted turtle	15X	5212367	N/A	N/A	1000	N/A
64	apaSpi1	286,620	1,931,078,847	1,877,982,184	53,096,663	% 29.87	Apalone spinifera		2306994	N/A	N/A	1000	N/A
65	pelSin1	19,904	2,202,483,752	2,106,639,384	95,844,368	% 33.82	Pelodiscus sinensis		3350749	N/A	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	RecipBest	7.627%	5000	loose
67	colLiv1	14,923	1,107,989,085	1,086,925,875	21,063,210	% 19.83	Columba livia		3148738	RecipBest	3.683%	5000	loose
68	falChe1	5,863	1,174,811,715	1,150,993,769	23,817,946	% 18.62	Falco cherrug		4154532	RecipBest	3.812%	5000	loose
69	falPer1	7,021	1,171,973,431	1,153,404,348	18,569,083	% 18.69	Falco peregrinus		3935757	RecipBest	3.879%	5000	loose
70	allMis1	14,645	2,174,259,888	2,128,720,123	45,539,765	% 37.18	American alligator		508966	RecipBest	7.084%	5000	loose
71	anaPla1	78,488	1,105,052,351	1,069,972,754	35,079,597	% 20.21	Anas platyrhynchos		1233631	RecipBest	3.509%	5000	loose
72	galGal4	15,932	1,046,932,099	1,032,854,810	14,077,289	% 20.41	Chicken	12X	90216835	RecipBest	3.684%	5000	loose
73	melGal1	5,891	1,061,817,101	935,922,386	125,894,715	% 6.60	Turkey	5X	74864452	SyntenicNet	2.645%	5000	loose
74	amaVit1	182,974	1,175,404,042	1,128,255,752	47,148,290	% 18.36	Parrot		19239	RecipBest	3.298%	5000	loose
75	araMac1	192,790	1,204,700,227	997,522,769	207,177,458	% 16.49	Ara macao		15974	RecipBest	2.912%	5000	loose
76	melUnd1	25,212	1,117,373,619	1,086,614,815	30,758,804	% 19.62	Budgerigar	7X	10614383	RecipBest	3.577%	5000	loose
77	ficAlb2	21,428	1,118,343,587	1,102,323,882	16,019,705	% 24.04	Ficedula albicollis		64724594	RecipBest	3.715%	5000	loose
78	anoCar2	6,457	1,799,143,587	1,701,353,767	97,789,820	% 41.98	Lizard	7.1X	150641573	SyntenicNet	3.552%	5000	loose
79	taeGut2	37,096	1,232,135,591	1,222,864,691	9,270,900	% 8.11	Zebra finch		62374962	RecipBest	5.321%	5000	loose
80	pseHum1	5,406	1,042,997,632	1,030,030,436	12,967,196	% 20.21	Pseudopodoces humilis		16337386	RecipBest	3.982%	5000	loose
81	geoFor1	27,239	1,065,292,181	1,041,286,029	24,006,152	% 19.99	Medium ground finch	115X	5255844	Net	3.503%	5000	loose
82	zonAlb1	6,018	1,052,600,561	1,006,293,510	46,307,051	% 20.03	Zonotrichia albicollis		4866725	RecipBest	3.476%	5000	loose
83	lepOcu1	1,925	945,874,548	869,414,359	76,460,189	% 24.85	Lepisosteus oculatus		50348508	N/A	N/A	1000	N/A
84	xenTro7	7,728	1,437,530,879	1,365,936,747	71,594,132	% 33.98	X. tropicalis		124127367	N/A	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	RecipBest	2.749%	5000	loose
86	gadMor1	427,428	824,327,835	608,038,555	216,289,280	% 31.25	Atlantic cod	40X	393166	N/A	N/A	1000	N/A
87	neoBri1	9,083	847,883,811	685,897,279	161,986,532	% 24.12	Neolamprologus brichardi		4430025	N/A	N/A	1000	N/A
88	oreNil2	5,678	927,696,114	816,084,674	111,611,440	% 25.51	Nile tilapia	269X	27159252	N/A	N/A	1000	N/A
89	gasAcu1	23	463,354,448	446,627,861	16,726,587	% 2.58	Stickleback	6X	20083130	Net	1.916%	5000	loose
90	tetNig2	27	358,618,246	302,314,788	56,303,458	% 20.27	Tetraodon	7.9X	13390619	Net	1.712%	5000	loose
91	hapBur1	7,994	831,398,301	698,936,397	132,461,904	% 24.10	Haplochromis burtoni		1194190	N/A	N/A	1000	N/A
92	takFla1	34,223	377,992,166	314,409,984	63,582,182	% 17.77	Takifugu flavidus		315240	N/A	N/A	1000	N/A
93	mayZeb1	3,725	849,595,388	713,527,863	136,067,525	% 25.04	Maylandia zebra		3702874	N/A	N/A	1000	N/A
94	punNye1	7,233	830,129,318	698,757,151	131,372,167	% 24.56	Pundamilia nyererei		2525540	N/A	N/A	1000	N/A
95	fr3	6,835	391,484,715	350,961,831	40,522,884	% 19.01	Fugu	8.5X	11516971	N/A	N/A	1000	N/A
96	astMex1	10,736	1,191,259,254	964,251,514	227,007,740	% 39.11	Astyanax mexicanus		1775308	N/A	N/A	1000	N/A
97	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	Net	2.790%	5000	loose
98	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	Net	1.849%	5000	loose
99	xipMac1	20,632	729,664,433	652,811,251	76,853,182	% 26.62	Xiphophorus maculatus		1303070	N/A	N/A	1000	N/A
100	petMar2	25,006	885,550,958	647,368,134	238,182,824	% 42.47	Lamprey	5.0X	184619	Net	1.046%	5000	loose