Hg19 100way Genome size statistics

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see also

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
01hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 referenceN/A N/A N/A
02panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 SyntenicNet95.279% 5000 medium
03gorGor3 46,823 3,029,553,6462,822,760,080 206,793,566% 48.80 Gorilla2.1X 145327772 RecipBest89.876% 5000 medium
04ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 RecipBest91.350% 5000 medium
05nomLeu3 17,492 2,962,077,4492,756,609,047 205,468,402% 51.14 Gibbon5.6X 117381234 SyntenicNet87.764% 5000 medium
06rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Rhesus50X 150158102 SyntenicNet82.859% 5000 medium
07macFas5 7,601 2,946,843,7372,803,866,385 142,977,352% 50.11 Macaca fascicularis68X 152835861 SyntenicNet86.666% 5000 medium
08papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 RecipBest82.810% 5000 medium
09chlSab1 2,004 2,789,656,3282,752,000,999 37,655,329% 48.77 Chlorocebus sabaeus95X 101219884 SyntenicNet86.446% 5000 medium
10calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet70.654% 5000 medium
11saiBol1 2,685 2,608,572,0642,477,131,095 131,440,969% 46.69 Squirrel monkey80X 18744880 SyntenicNet69.598% 5000 medium
12otoGar3 7,793 2,519,724,5502,359,530,453 160,194,097% 39.51 Bushbaby137X 13852661 SyntenicNet54.830% 3000 medium
13tupChi1 50,750 2,846,580,2352,706,389,135 140,191,100% 40.02 Tupaia chinensis80X 3670124 SyntenicNet46.558% 3000 medium
14speTri2 12,483 2,478,393,7702,311,060,300 167,333,470% 36.27 Squirrel495X 8192786 SyntenicNet49.723% 3000 medium
15jacJac1 10,896 2,835,242,7672,470,259,869 364,982,898% 37.29 Jaculus jaculus78X 22080993 SyntenicNet35.106% 3000 medium
16micOch1 6,335 2,287,340,9432,104,321,675 183,019,268% 23.89 Microtus ochrogaster94X 61813736 SyntenicNet32.285% 3000 medium
17criGri1 52,711 2,360,146,4282,301,325,917 58,820,511% 26.43 Cricetulus griseus130X 1558295 SyntenicNet33.985% 3000 medium
18mesAur1 21,484 2,504,925,0392,076,176,254 428,748,785% 25.70 Mesocricetus auratus115X 12753307 SyntenicNet31.606% 3000 medium
19mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 SyntenicNet35.249% 3000 medium
20rn5 2,739 2,909,698,9382,572,853,723 336,845,215% 42.81 Rat6X 154597545 SyntenicNet31.662% 3000 medium
21hetGla2 4,229 2,618,204,6392,314,771,103 303,433,536% 32.31 Naked mole-rat90X 20532749 SyntenicNet47.600% 3000 medium
22cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 SyntenicNet43.680% 3000 medium
23chiLan1 2,838 2,390,852,3912,284,276,400 106,575,991% 30.82 Chinchilla87X 21893125 SyntenicNet47.012% 3000 medium
24octDeg1 7,134 2,995,882,9382,526,254,692 469,628,246% 26.47 Octodon degus80X 12091372 SyntenicNet41.385% 3000 medium
25oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 SyntenicNet44.317% 3000 medium
26ochPri3 10,420 2,229,835,7161,943,987,870 285,847,846% 29.53 Pika103X 26863993 SyntenicNet34.676% 3000 medium
27susScr3 4,583 2,808,525,9912,518,987,191 289,538,800% 44.30 Pig24X 148491826 SyntenicNet45.977% 3000 medium
28vicPac2 276,611 2,172,177,9942,078,582,856 93,595,138% 35.40 Alpaca22X 7263804 SyntenicNet50.193% 3000 medium
29camFer1 13,334 2,009,194,6091,985,416,433 23,778,176% 33.32 Camelus ferus30X 2005940 SyntenicNet50.419% 3000 medium
30turTru2 240,901 2,551,996,5732,332,402,443 219,594,130% 43.56 Dolphin3.5X 116261 RecipBest51.158% 3000 medium
31orcOrc1 1,668 2,372,919,8772,249,582,112 123,337,765% 42.47 Orcinus orca200X 12735091 SyntenicNet52.072% 3000 medium
32panHod1 15,059 2,696,886,3302,507,986,438 188,899,892% 42.51 Pantholops hodgsonii67X 2772860 SyntenicNet46.863% 3000 medium
33bosTau7 11,692 2,981,119,5792,804,673,174 176,446,405% 49.56 Cow7.1X 85119472 SyntenicNet46.971% 3000 medium
34oviAri3 5,698 2,619,054,3882,534,335,866 84,718,522% 45.18 Sheep142X 100079507 SyntenicNet46.833% 3000 medium
35capHir1 77,021 2,635,848,9002,495,939,845 139,909,055% 43.55 Capra hircus86.64X 92306894 SyntenicNet46.498% 3000 medium
36equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet57.050% 3000 medium
37cerSim1 3,087 2,464,367,1802,366,858,012 97,509,168% 38.80 White rhinoceros91X 26277727 SyntenicNet58.103% 3000 medium
38felCat5 5,500 2,455,541,1362,364,296,207 91,244,929% 43.24 Cat12X 148491654 SyntenicNet52.426% 3000 medium
39canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 SyntenicNet51.848% 3000 medium
40musFur1 7,741 2,410,758,0132,277,906,570 132,851,443% 38.98 Ferret 162X 9335154 SyntenicNet50.993% 3000 medium
41ailMel1 81,467 2,299,509,0152,245,312,831 54,196,184% 38.96 Panda73X 1281781 SyntenicNet50.022% 3000 medium
42odoRosDiv1 3,892 2,400,133,6282,300,235,509 99,898,119% 40.52 Odobenus rosmarus divergens200X 2616778 SyntenicNet53.559% 3000 medium
43lepWed1 16,711 3,156,902,7622,223,164,129 933,738,633% 40.09 Leptonychotes weddellii82X 904031 RecipBest52.424% 3000 medium
44pteAle1 65,597 1,985,958,7071,944,625,202 41,333,505% 32.56 Pteropus alecto110X 15954802 SyntenicNet49.670% 3000 medium
45pteVam1 96,944 1,996,076,4101,839,436,660 156,639,750% 31.75 Megabat2X 124060 RecipBest45.414% 3000 medium
46myoDav1 101,769 2,059,799,7081,878,461,987 181,337,721% 23.35 Myotis Davidii110X 3454484 SyntenicNet39.790% 3000 medium
47myoLuc2 11,654 2,034,575,3001,966,419,868 68,155,432% 33.71 Microbat2.18X 4293315 SyntenicNet39.886% 3000 medium
48eptFus1 6,788 2,026,627,1851,811,378,799 215,248,386% 24.11 Eptesicus fuscus84X 13454942 SyntenicNet40.221% 3000 medium
49eriEur2 5,803 2,715,720,9252,333,073,535 382,647,390% 45.60 Hedgehog79X 3264618 SyntenicNet26.149% 3000 medium
50sorAra2 12,845 2,423,158,1832,192,103,426 231,054,757% 32.76 Shrew120X 22794405 SyntenicNet27.681% 3000 medium
51conCri1 2,038 1,769,657,8971,682,542,007 87,115,890% 18.21 Condylura cristata113.1X 55520359 SyntenicNet37.034% 3000 medium
52loxAfr3 2,353 3,196,760,8333,118,565,340 78,195,493% 47.63 Elephant7X 46401353 SyntenicNet46.636% 3000 medium
53eleEdw1 8,768 3,843,982,8613,315,871,847 528,111,014% 49.11 Elephantulus edwardii62X 15011382 SyntenicNet27.675% 3000 medium
54triMan1 6,323 3,103,808,4062,769,099,677 334,708,729% 36.24 Manatee150X 14442683 SyntenicNet46.580% 3000 medium
55chrAsi1 20,500 4,210,110,4583,363,564,316 846,546,142% 20.11 Chrysochloris asiatica66X 13470186 SyntenicNet34.209% 3000 medium
56echTel2 8,402 2,947,024,2862,605,196,361 341,827,925% 28.26 Tenrec78X 45764842 SyntenicNet30.135% 3000 medium
57oryAfe1 22,509 4,444,080,5273,415,340,621 1,028,739,906% 31.09 Orycteropus afer44X 7875832 SyntenicNet41.668% 3000 medium
58dasNov3 46,559 3,631,522,7113,299,882,028 331,640,683% 49.28 Armadillo6X 1687935 SyntenicNet46.571% 3000 medium
59monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 Net14.358% 5000 loose
60sarHar1 35,974 3,174,693,0102,931,539,702 243,153,308% 39.66 Tasmanian devil85X 1847106 Net7.414% 5000 loose
61macEug2 277,711 3,075,184,0242,536,076,954 539,107,070% 47.39 Wallaby2X 36602 RecipBest6.534% 5000 loose
62ornAna1 201,523 1,996,811,2121,842,235,522 154,575,690% 47.89 Platypus6X 991605 RecipBest7.627% 5000 loose
63falChe1 5,863 1,174,811,7151,150,993,769 23,817,946% 18.62 Falco cherrug147X 4154532 Net3.812% 5000 loose
64falPer1 7,021 1,171,973,4311,153,404,348 18,569,083% 18.69 Falco peregrinus137.6X 3935757 Net3.879% 5000 loose
65ficAlb2 21,428 1,118,343,5871,102,323,882 16,019,705% 24.04 Ficedula albicollis60X 64724594 Net3.715% 5000 loose
66zonAlb1 6,018 1,052,600,5611,006,293,510 46,307,051% 20.03 Zonotrichia albicollis63X 4866725 Net3.476% 5000 loose
67geoFor1 27,239 1,065,292,1811,041,286,029 24,006,152% 19.99 Medium ground finch115X 5255844 Net3.503% 5000 loose
68taeGut2 37,096 1,232,135,5911,222,864,691 9,270,900% 8.11 Zebra finch5.5X 62374962 Net5.321% 5000 loose
69pseHum1 5,406 1,042,997,6321,030,030,436 12,967,196% 20.21 Pseudopodoces humilis96.25X 16337386 Net3.982% 5000 loose
70melUnd1 25,212 1,117,373,6191,086,614,815 30,758,804% 19.62 Budgerigar7X 10614383 Net3.577% 5000 loose
71amaVit1 182,974 1,175,404,0421,128,255,752 47,148,290% 18.36 Parrot24X 19239 Net3.298% 5000 loose
72araMac1 192,790 1,204,700,227997,522,769 207,177,458% 16.49 Ara macao26X 15974 Net2.912% 5000 loose
73colLiv1 14,923 1,107,989,0851,086,925,875 21,063,210% 19.83 Columba livia60X 3148738 Net3.683% 5000 loose
74anaPla1 78,488 1,105,052,3511,069,972,754 35,079,597% 20.21 Anas platyrhynchos60X 1233631 Net3.509% 5000 loose
75galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 Net3.684% 5000 loose
76melGal1 5,891 1,061,817,101935,922,386 125,894,715% 6.60 Turkey5X 74864452 Net2.645% 5000 loose
77allMis1 14,645 2,174,259,8882,128,720,123 45,539,765% 37.18 American alligator68X 508966 Net7.084% 5000 loose
78cheMyd1 140,023 2,208,410,3772,110,381,997 98,028,380% 29.65 Chelonia mydas110X 3864108 Net3.696% 5000 loose
79chrPic1 80,984 2,589,745,7042,158,289,746 431,455,958% 31.20 Painted turtle15X 5212367 Net3.716% 3000 medium
80pelSin1 19,904 2,202,483,7522,106,639,384 95,844,368% 33.82 Pelodiscus sinensis105X 3350749 Net3.268% 3000 medium
81apaSpi1 286,620 1,931,078,8471,877,982,184 53,096,663% 29.87 Apalone spinifera33.4X 2306994 Net2.952% 5000 loose
82anoCar2 6,457 1,799,143,5871,701,353,767 97,789,820% 41.98 Lizard7.1X 150641573 Net3.552% 5000 loose
83xenTro7 7,728 1,437,530,8791,365,936,747 71,594,132% 33.98 X. tropicalis7.44X 124127367 Net3.153% 5000 loose
84latCha1 22,819 2,860,591,9212,183,592,768 676,999,153% 45.68 Coelacanth77.5X 924513 Net2.749% 5000 loose
85tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 Net1.712% 5000 loose
86fr3 6,835 391,484,715350,961,831 40,522,884% 19.01 Fugu8.5X 11516971 Net1.703% 5000 loose
87takFla1 34,223 377,992,166314,409,984 63,582,182% 17.77 Takifugu flavidus131X 315240 Net1.062% 5000 loose
88oreNil2 5,678 927,696,114816,084,674 111,611,440% 25.51 Nile tilapia269X 27159252 Net1.832% 5000 loose
89neoBri1 9,083 847,883,811685,897,279 161,986,532% 24.12 Neolamprologus brichardi171X 4430025 Net1.218% 5000 loose
90hapBur1 7,994 831,398,301698,936,397 132,461,904% 24.10 Haplochromis burtoni131X 1194190 Net1.221% 5000 loose
91mayZeb1 3,725 849,595,388713,527,863 136,067,525% 25.04 Maylandia zebra129.7X 3702874 Net1.243% 5000 loose
92punNye1 7,233 830,129,318698,757,151 131,372,167% 24.56 Pundamilia nyererei126X 2525540 Net1.219% 5000 loose
93oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net1.849% 5000 loose
94xipMac1 20,632 729,664,433652,811,251 76,853,182% 26.62 Xiphophorus maculatus19.6X 1303070 Net1.842% 5000 loose
95gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 Net1.916% 5000 loose
96gadMor1 427,428 824,327,835608,038,555 216,289,280% 31.25 Atlantic cod40X 393166 Net1.551% 5000 loose
97danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net2.790% 5000 loose
98astMex1 10,736 1,191,259,254964,251,514 227,007,740% 39.11 Astyanax mexicanus70X 1775308 Net1.269% 5000 loose
99lepOcu1 1,925 945,874,548869,414,359 76,460,189% 24.85 Lepisosteus oculatus677.5X 50348508 Net1.522% 5000 loose
100petMar2 25,006 885,550,958647,368,134 238,182,824% 42.47 Lamprey5.0X 184619 Net1.046% 5000 loose