Hg19 100way Genome size statistics

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Revision as of 21:50, 20 August 2013 by Hiram (talk | contribs) (updating with a couple new results)
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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 N/AN/A N/A N/A
02panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 RecipBest95.279% 5000 medium
03gorGor3 46,823 3,029,553,6462,822,760,080 206,793,566% 48.80 Gorilla2.1X 145327772 SyntenicNet89.876% 5000 medium
04ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet91.350% 5000 medium
05nomLeu3 17,492 2,962,077,4492,756,609,047 205,468,402% 51.14 Gibbon  117381234 SyntenicNet87.764% 5000 medium
06chlSab1 2,004 2,789,656,3282,752,000,999 37,655,329% 48.77 Chlorocebus sabaeus  101219884 RecipBest86.446% 5000 medium
07macFas5 7,601 2,946,843,7372,803,866,385 142,977,352% 50.11 Macaca fascicularis  152835861 RecipBest86.666% 5000 medium
08rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Rhesus50X 150158102 SyntenicNet82.859% 5000 medium
09papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 RecipBest82.810% 5000 medium
10saiBol1 2,685 2,608,572,0642,477,131,095 131,440,969% 46.69 Squirrel monkey80X 18744880 RecipBest69.598% 5000 medium
11calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet70.654% 5000 medium
12otoGar3 7,793 2,519,724,5502,359,530,453 160,194,097% 39.51 Bushbaby137X 13852661 RecipBest54.830% 3000 medium
13tupChi1 50,750 2,846,580,2352,706,389,135 140,191,100% 40.02 Tupaia chinensis  3670124 RecipBest46.558% 3000 medium
14cerSim1 3,087 2,464,367,1802,366,858,012 97,509,168% 38.80 White rhinoceros  26277727 Net58.103% 3000 medium
15equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet57.050% 3000 medium
16camFer1 13,334 2,009,194,6091,985,416,433 23,778,176% 33.32 Camelus ferus  2005940 RecipBest50.419% 3000 medium
17vicPac2 276,611 2,172,177,9942,078,582,856 93,595,138% 35.40 Alpaca  7263804 RecipBest50.193% 3000 medium
18orcOrc1 1,668 2,372,919,8772,249,582,112 123,337,765% 42.47 Orcinus orca  12735091 RecipBestN/A 3000 medium
19turTru2 240,901 2,551,996,5732,332,402,443 219,594,130% 43.56 Dolphin3.5X 116261 RecipBest51.158% 3000 medium
20musFur1 7,741 2,410,758,0132,277,906,570 132,851,443% 38.98 Ferret   9335154 RecipBest50.993% 3000 medium
21oryAfe1 22,509 4,444,080,5273,415,340,621 1,028,739,906% 31.09 Orycteropus afer  7875832 RecipBest41.668% 3000 medium
22speTri2 12,483 2,478,393,7702,311,060,300 167,333,470% 36.27 Squirrel495X 8192786 N/AN/A 1000 N/A
23pteAle1 65,597 1,985,958,7071,944,625,202 41,333,505% 32.56 Pteropus alecto  15954802 N/AN/A 1000 N/A
24susScr3 4,583 2,808,525,9912,518,987,191 289,538,800% 44.30 Pig24X 148491826 N/AN/A 1000 N/A
25triMan1 6,323 3,103,808,4062,769,099,677 334,708,729% 36.24 Manatee150X 14442683 RecipBest46.580% 3000 medium
26octDeg1 7,134 2,995,882,9382,526,254,692 469,628,246% 26.47 Octodon degus  12091372 RecipBest41.385% 3000 medium
27pteVam1 96,944 1,996,076,4101,839,436,660 156,639,750% 31.75 Megabat2X 124060 RecipBest45.414% 3000 medium
28loxAfr3 2,353 3,196,760,8333,118,565,340 78,195,493% 47.63 Elephant7X 46401353 SyntenicNet46.636% 3000 medium
29felCat5 5,500 2,455,541,1362,364,296,207 91,244,929% 43.24 Cat12X 148491654 RecipBest52.426% 3000 medium
30ailMel1 81,467 2,299,509,0152,245,312,831 54,196,184% 38.96 Panda73X 1281781 SyntenicNet50.022% 3000 medium
31canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 SyntenicNet51.848% 3000 medium
32chrAsi1 20,500 4,210,110,4583,363,564,316 846,546,142% 20.11 Chrysochloris asiatica  13470186 RecipBest34.209% 3000 medium
33dasNov3 46,559 3,631,522,7113,299,882,028 331,640,683% 49.28 Armadillo6X 1687935 RecipBest46.571% 3000 medium
34oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 SyntenicNet44.317% 3000 medium
35myoDav1 101,769 2,059,799,7081,878,461,987 181,337,721% 23.35 Myotis Davidii  3454484 N/AN/A 1000 N/A
36panHod1 15,059 2,696,886,3302,507,986,438 188,899,892% 42.51 Pantholops hodgsonii  2772860 RecipBest46.863% 3000 medium
37lepWed1 16,711 3,156,902,7622,223,164,129 933,738,633% 40.09 Leptonychotes weddellii  904031 RecipBest52.424% 3000 medium
38odoRosDiv1 3,892 2,400,133,6282,300,235,509 99,898,119% 40.52 Odobenus rosmarus divergens  2616778 RecipBest53.559% 3000 medium
39myoLuc2 11,654 2,034,575,3001,966,419,868 68,155,432% 33.71 Microbat2.18X 4293315 N/AN/A 1000 N/A
40eptFus1 6,788 2,026,627,1851,811,378,799 215,248,386% 24.11 Eptesicus fuscus  13454942 N/AN/A 1000 N/A
41bosTau7 11,692 2,981,119,5792,804,673,174 176,446,405% 49.56 Cow7.1X 85119472 SyntenicNet46.971% 3000 medium
42capHir1 77,021 2,635,848,9002,495,939,845 139,909,055% 43.55 Capra hircus  92306894 RecipBest46.498% 3000 medium
43oviAri3 5,698 2,619,054,3882,534,335,866 84,718,522% 45.18 Sheep  100079507 RecipBest46.833% 3000 medium
44hetGla2 4,229 2,618,204,6392,314,771,103 303,433,536% 32.31 Naked mole-rat90X 20532749 RecipBest47.600% 3000 medium
45eleEdw1 8,768 3,843,982,8613,315,871,847 528,111,014% 49.11 Elephantulus edwardii  15011382 RecipBest27.675% 3000 medium
46jacJac1 10,896 2,835,242,7672,470,259,869 364,982,898% 37.29 Jaculus jaculus  22080993 RecipBest35.106% 3000 medium
47chiLan1 2,838 2,390,852,3912,284,276,400 106,575,991% 30.82 Chinchilla  21893125 N/AN/A 1000 N/A
48cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 SyntenicNet43.680% 3000 medium
49conCri1 2,038 1,769,657,8971,682,542,007 87,115,890% 18.21 Condylura cristata  55520359 RecipBest37.034% 3000 medium
50ochPri3 10,420 2,229,835,7161,943,987,870 285,847,846% 29.53 Pika  26863993 RecipBest34.676% 3000 medium
51eriEur2 5,803 2,715,720,9252,333,073,535 382,647,390% 45.60 Hedgehog  3264618 RecipBest26.149% 3000 medium
52echTel2 8,402 2,947,024,2862,605,196,361 341,827,925% 28.26 Tenrec  45764842 RecipBest30.135% 3000 medium
53mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 RecipBest35.249% 3000 medium
54rn5 2,739 2,909,698,9382,572,853,723 336,845,215% 42.81 Rat6X 154597545 SyntenicNet31.662% 3000 medium
55criGri1 52,711 2,360,146,4282,301,325,917 58,820,511% 26.43 Cricetulus griseus  1558295 N/AN/A 1000 N/A
56mesAur1 21,484 2,504,925,0392,076,176,254 428,748,785% 25.70 Mesocricetus auratus  12753307 N/AN/A 1000 N/A
57micOch1 6,335 2,287,340,9432,104,321,675 183,019,268% 23.89 Microtus ochrogaster  61813736 N/AN/A 1000 N/A
58sorAra2 12,845 2,423,158,1832,192,103,426 231,054,757% 32.76 Shrew  22794405 RecipBest27.681% 3000 medium
59macEug2 277,711 3,075,184,0242,536,076,954 539,107,070% 47.39 Wallaby2X 36602 RecipBest6.534% 5000 loose
60monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 SyntenicNet14.358% 5000 loose
61sarHar1 35,974 3,174,693,0102,931,539,702 243,153,308% 39.66 Tasmanian devil85X 1847106 RecipBest7.414% 5000 loose
62apaSpi1 286,620 1,931,078,8471,877,982,184 53,096,663% 29.87 Apalone spinifera  2306994 N/AN/A 1000 N/A
63cheMyd1 140,023 2,208,410,3772,110,381,997 98,028,380% 29.65 Chelonia mydas  3864108 N/AN/A 1000 N/A
64chrPic1 80,984 2,589,745,7042,158,289,746 431,455,958% 31.20 Painted turtle15X 5212367 N/AN/A 1000 N/A
65pelSin1 19,904 2,202,483,7522,106,639,384 95,844,368% 33.82 Pelodiscus sinensis  3350749 N/AN/A 1000 N/A
66ornAna1 201,523 1,996,811,2121,842,235,522 154,575,690% 47.89 Platypus6X 991605 RecipBest7.627% 5000 loose
67allMis1 14,645 2,174,259,8882,128,720,123 45,539,765% 37.18 American alligator  508966 RecipBest7.084% 5000 loose
68anaPla1 78,488 1,105,052,3511,069,972,754 35,079,597% 20.21 Anas platyrhynchos  1233631 RecipBest3.509% 5000 loose
69colLiv1 14,923 1,107,989,0851,086,925,875 21,063,210% 19.83 Columba livia  3148738 RecipBest3.683% 5000 loose
70galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 RecipBest3.684% 5000 loose
71anoCar2 6,457 1,799,143,5871,701,353,767 97,789,820% 41.98 Lizard7.1X 150641573 SyntenicNet3.552% 5000 loose
72melGal1 5,891 1,061,817,101935,922,386 125,894,715% 6.60 Turkey5X 74864452 SyntenicNet2.645% 5000 loose
73falChe1 5,863 1,174,811,7151,150,993,769 23,817,946% 18.62 Falco cherrug  4154532 RecipBest3.812% 5000 loose
74falPer1 7,021 1,171,973,4311,153,404,348 18,569,083% 18.69 Falco peregrinus  3935757 RecipBest3.879% 5000 loose
75amaVit1 182,974 1,175,404,0421,128,255,752 47,148,290% 18.36 Parrot  19239 RecipBest3.298% 5000 loose
76araMac1 192,790 1,204,700,227997,522,769 207,177,458% 16.49 Ara macao  15974 RecipBest2.912% 5000 loose
77melUnd1 25,212 1,117,373,6191,086,614,815 30,758,804% 19.62 Budgerigar7X 10614383 RecipBest3.577% 5000 loose
78pseHum1 5,406 1,042,997,6321,030,030,436 12,967,196% 20.21 Pseudopodoces humilis  16337386 RecipBest3.982% 5000 loose
79zonAlb1 6,018 1,052,600,5611,006,293,510 46,307,051% 20.03 Zonotrichia albicollis  4866725 RecipBest3.476% 5000 loose
80ficAlb2 21,428 1,118,343,5871,102,323,882 16,019,705% 24.04 Ficedula albicollis  64724594 RecipBest3.715% 5000 loose
81geoFor1 27,239 1,065,292,1811,041,286,029 24,006,152% 19.99 Medium ground finch115X 5255844 Net3.503% 5000 loose
82taeGut2 37,096 1,232,135,5911,222,864,691 9,270,900% 8.11 Zebra finch  62374962 RecipBest5.321% 5000 loose
83lepOcu1 1,925 945,874,548869,414,359 76,460,189% 24.85 Lepisosteus oculatus  50348508 N/AN/A 1000 N/A
84xenTro7 7,728 1,437,530,8791,365,936,747 71,594,132% 33.98 X. tropicalis  124127367 N/AN/A 1000 N/A
85latCha1 22,819 2,860,591,9212,183,592,768 676,999,153% 45.68 Coelacanth77.5X 924513 RecipBest2.749% 5000 loose
86gadMor1 427,428 824,327,835608,038,555 216,289,280% 31.25 Atlantic cod40X 393166 N/AN/A 1000 N/A
87neoBri1 9,083 847,883,811685,897,279 161,986,532% 24.12 Neolamprologus brichardi  4430025 N/AN/A 1000 N/A
88oreNil2 5,678 927,696,114816,084,674 111,611,440% 25.51 Nile tilapia269X 27159252 N/AN/A 1000 N/A
89gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 Net1.916% 5000 loose
90tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 Net1.712% 5000 loose
91hapBur1 7,994 831,398,301698,936,397 132,461,904% 24.10 Haplochromis burtoni  1194190 N/AN/A 1000 N/A
92takFla1 34,223 377,992,166314,409,984 63,582,182% 17.77 Takifugu flavidus  315240 N/AN/A 1000 N/A
93mayZeb1 3,725 849,595,388713,527,863 136,067,525% 25.04 Maylandia zebra  3702874 N/AN/A 1000 N/A
94punNye1 7,233 830,129,318698,757,151 131,372,167% 24.56 Pundamilia nyererei  2525540 N/AN/A 1000 N/A
95fr3 6,835 391,484,715350,961,831 40,522,884% 19.01 Fugu8.5X 11516971 NetN/A 5000 loose
96astMex1 10,736 1,191,259,254964,251,514 227,007,740% 39.11 Astyanax mexicanus  1775308 N/AN/A 1000 N/A
97danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 Net2.790% 5000 loose
98oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 Net1.849% 5000 loose
99xipMac1 20,632 729,664,433652,811,251 76,853,182% 26.62 Xiphophorus maculatus  1303070 N/AN/A 1000 N/A
100petMar2 25,006 885,550,958647,368,134 238,182,824% 42.47 Lamprey5.0X 184619 Net1.046% 5000 loose