Genome size statistics: Difference between revisions

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(updated status)
(added caption for hg18 matched)
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<LI>total size == all bases in assembly, N and non-N</LI>
<LI>total size == all bases in assembly, N and non-N</LI>
<LI>% masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats</LI>
<LI>% masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats</LI>
<LI>% of hg18 matched (chainLink table) == featureBits hg18 chain<Db>Link == alignment coverage</LI>
</UL>
</UL>



Revision as of 18:37, 29 October 2008

see also

Hg18 44way alignment

statistics collected from UCSC 2bit files

  • 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
  • % masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats
  • % of hg18 matched (chainLink table) == featureBits hg18 chain<Db>Link == alignment coverage

do not edit, automatically generated table

order
count
ucsc
db name
chrom
count
total
size
non-N
bases
N base
count
% masked common name % of hg18
matched
(chainLink table)
01hg1849 3,107,677,2732,881,421,696 226,255,577% 48.85 HumanN/A
02panTro252 3,350,447,5122,909,246,738 441,200,774% 48.90 Chimp94.888%
03 gorGor1to be done
04ponAbe255 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan92.892%
05rheMac222 2,864,106,0712,646,668,809 217,437,262% 48.28 Rhesus85.552%
06calJac149,724 3,029,401,8402,929,124,957 100,276,883% 47.50 Marmoset78.351%
07tarSyr1656,709 3,179,905,1322,768,536,343 411,368,789% 41.75 Tarsier47.999%
08otoGar1120,882 3,420,058,8641,969,052,059 1,451,006,805% 34.89 Bushbaby44.638%
09micMur1185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur46.445%
10tupBel1150,851 3,660,774,9572,137,225,476 1,523,549,481% 20.43 TreeShrew37.348%
11mm935 2,725,765,4812,620,345,972 105,419,509% 44.09 Mouse35.201%
12rn445 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat32.893%
13dipOrd1210,053 2,158,502,0981,844,961,421 313,540,677% 28.28 Kangaroo rat27.282%
14cavPor33,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea Pig43.971%
15speTri1160,889 3,488,768,5921,913,367,893 1,575,400,699% 26.90 Squirrel35.828%
16oryCun1215,471 3,464,410,0392,076,044,328 1,388,365,711% 37.44 Rabbit34.015%
17ochPri2187,558 3,445,784,3541,923,624,051 1,522,160,303% 11.44 Pika27.974%
18sorAra1262,057 2,936,119,0081,832,864,697 1,103,254,311% 39.07 Shrew20.056%
19eriEur1379,802 3,367,787,3582,133,134,836 1,234,652,522% 50.89 hedgehog19.622%
20felCat3217,790 4,045,535,3221,642,698,377 2,402,836,945% 37.66 Cat35.888%
21canFam241 2,531,673,9532,384,996,543 146,677,410% 40.63 Dog52.915%
22equCab234 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse57.162%
23pteVam196,944 1,996,076,4101,839,436,660 156,639,750% 31.75 Megabat45.502%
24myoLuc1193,323 2,850,051,5591,673,855,868 1,176,195,691% 24.90 Microbat33.044%
25turTru1116,467 2,519,048,4862,298,444,090 220,604,396% 43.86 Dolphin48.537%
26bosTau411,900 2,917,974,5302,731,813,236 186,161,294% 46.89 Cow46.689%
27vicPac1298,413 2,962,253,6081,922,910,435 1,039,343,173% 32.24 Alpaca39.531%
28dasNov2292,141 4,813,823,5622,371,493,872 2,442,329,690% 37.23 Armadillo33.663%
29choHof1481,259 2,458,927,6202,060,419,685 398,507,935% 35.67 Sloth34.463%
30echTel1325,491 3,823,724,7282,111,581,369 1,712,143,359% 13.84 Tenrec23.645%
31loxAfr2225,378 4,170,414,8522,444,975,542 1,725,439,310% 44.13 Elephant35.204%
32proCap1295,006 2,985,258,9992,407,847,681 577,411,318% 28.11 Rock hyrax30.935%
33monDom410 3,605,614,6493,501,643,220 103,971,429% 55.69 Opossum12.385%
34ornAna1201,523 1,996,811,2121,842,235,522 154,575,690% 47.89 Platypus7.870%
35galGal357 1,100,480,4411,042,583,135 57,897,306% 9.85 Chicken3.589%
36taeGut170 1,233,186,3411,222,864,691 10,321,650% 20.42 Zebra finch3.503%
37anoCar17,233 1,781,602,8991,741,478,929 40,123,970% 42.56 Lizard4.774%
38xenTro219,759 1,513,925,4921,359,400,017 154,525,475% 19.65 X. tropicalis2.623%
39danRer55,036 1,440,582,3081,435,595,672 4,986,636% 49.53 Zebrafish2.565%
40tetNig127 402,240,326312,394,419 89,845,907% 4.34 Tetraodon2.001%
41fr22 400,525,790351,212,245 49,313,545% 19.01 Fugu1.766%
42gasAcu123 463,354,448446,627,861 16,726,587% 2.58 Stickleback1.923%
43oryLat27,189 869,000,216700,386,597 168,613,619% 33.09 Medaka1.829%
44petMar1108,241 1,027,258,967831,696,438 195,562,529% 40.67 Lamprey1.251%