Mm10 Genome size statistics: Difference between revisions

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(updated data)
(updated data)
Line 314: Line 314:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAGV00 Armadillo]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAGV00 Armadillo]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>55360</TH>
<TH ALIGN=CENTER>55360</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>17.004%</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/614 32]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/614 32]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]</TH>
<TH ALIGN=RIGHT>11,654</TH>
<TH ALIGN=RIGHT>11,654</TH>
Line 350: Line 350:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRQ00 Rock hyrax]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRQ00 Rock hyrax]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>24297</TH>
<TH ALIGN=CENTER>24297</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>15.147%</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/771 36]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri2 ochPri2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/771 36]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri2 ochPri2]</TH>
<TH ALIGN=RIGHT>187,558</TH>
<TH ALIGN=RIGHT>187,558</TH>
Line 359: Line 359:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/74593 Pika]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/74593 Pika]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>88760</TH>
<TH ALIGN=CENTER>88760</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><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>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/hedgehog/eriEur1/ 37]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur1 eriEur1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/hedgehog/eriEur1/ 37]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur1 eriEur1]</TH>
<TH ALIGN=RIGHT>379,802</TH>
<TH ALIGN=RIGHT>379,802</TH>
Line 368: Line 368:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/genome/227 Hedgehog]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/genome/227 Hedgehog]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>33565</TH>
<TH ALIGN=CENTER>33565</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>9.856%</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>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tenrec/echTel1/ 38]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel1 echTel1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tenrec/echTel1/ 38]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel1 echTel1]</TH>
<TH ALIGN=RIGHT>325,491</TH>
<TH ALIGN=RIGHT>325,491</TH>
Line 377: Line 377:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAIY00 Tenrec]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAIY00 Tenrec]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>48377</TH>
<TH ALIGN=CENTER>48377</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>10.947%</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>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/commonShrew/sorAra1/ 39]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra1 sorAra1]</TH>
<TR><TH ALIGN=RIGHT>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/commonShrew/sorAra1/ 39]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra1 sorAra1]</TH>
<TH ALIGN=RIGHT>262,057</TH>
<TH ALIGN=RIGHT>262,057</TH>
Line 386: Line 386:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/genome/91 Shrew]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/genome/91 Shrew]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>47941</TH>
<TH ALIGN=CENTER>47941</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>9.382%</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/233 40]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macEug2 macEug2]</TH>
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/233 40]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macEug2 macEug2]</TH>
<TH ALIGN=RIGHT>277,711</TH>
<TH ALIGN=RIGHT>277,711</TH>
Line 395: Line 395:
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQO00 Wallaby]</TD><TH ALIGN=CENTER>2X</TH>
   <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQO00 Wallaby]</TD><TH ALIGN=CENTER>2X</TH>
<TH ALIGN=CENTER>36602</TH>
<TH ALIGN=CENTER>36602</TH>
   <TD ALIGN=CENTER>in progress</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD ALIGN=CENTER>SyntenicNet</TD><TD ALIGN=RIGHT>4.353%</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.broadinstitute.org/mammals/opossum 41]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH>
<TR><TH ALIGN=RIGHT>[http://www.broadinstitute.org/mammals/opossum 41]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH>
<TH ALIGN=RIGHT>11</TH>
<TH ALIGN=RIGHT>11</TH>

Revision as of 17:04, 26 March 2012

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 mm10
matched
(chainLink table)
chain
minScore
chain
linearGap
01mm10 66 2,730,871,7742,652,783,500 78,088,274% 45.18 Mouse20X 130694993 N/AN/A N/A N/A
02rn4 45 2,834,127,2932,566,294,765 267,832,528% 44.29 Rat20X 143002779 SyntenicNet54.645% 5000 medium
03speTri2 12,483 2,478,393,7702,311,060,300 167,333,470% 36.27 Squirrel495X 8192786 SyntenicNet34.217% 3000 medium
04micMur1 185,042 2,902,270,7361,852,394,361 1,049,876,375% 37.31 Mouse lemur2X 140884 SyntenicNet26.636% 3000 medium
05dipOrd1 210,053 2,158,502,0981,844,961,421 313,540,677% 28.28 Kangaroo rat2X 36427 SyntenicNet19.460% 3000 medium
06saiBol1 2,685 2,608,572,0642,477,131,095 131,440,969% 46.69 Squirrel monkey80X 18744880 SyntenicNet32.339% 3000 medium
07hetGla1 39,267 2,643,978,2232,430,064,805 213,913,418% 32.64 Naked mole-rat90X 1603177 SyntenicNet32.163% 3000 medium
08hg19 93 3,137,161,2642,897,310,462 239,850,802% 50.63 Human20X 146364022 SyntenicNet38.226% 3000 medium
09gorGor3 46,823 3,029,553,6462,822,760,080 206,793,566% 48.80 Gorilla2.1X 145327772 SyntenicNet33.987% 3000 medium
10panTro4 24,129 3,309,577,9222,902,338,967 407,238,955% 51.29 Chimp6X 143986469 SyntenicNet34.674% 3000 medium
11nomLeu1 17,968 2,936,035,3332,756,591,777 179,443,556% 50.82 Gibbon5.6X 22692035 SyntenicNet34.132% 3000 medium
12ponAbe2 55 3,446,771,3963,093,543,172 353,228,224% 50.89 Orangutan6X 135191526 SyntenicNet34.496% 3000 medium
13tarSyr1 656,709 3,179,905,1322,768,536,343 411,368,789% 41.75 Tarsier2X 12214 SyntenicNet24.560% 3000 medium
14rheMac3 34,103 2,969,988,1802,639,145,830 330,842,350% 48.54 Chinese rhesus50X 150158102 SyntenicNet33.931% 3000 medium
15papHam1 387,374 2,867,564,6542,741,849,051 125,715,603% 48.70 Baboon5.3X 88525 SyntenicNet33.577% 3000 medium
16otoGar3 7,793 2,519,724,5502,359,530,453 160,194,097% 39.51 Bushbaby137X 13852661 SyntenicNet29.795% 3000 medium
17calJac3 14,205 2,914,958,5442,752,505,800 162,452,744% 47.71 Marmoset6X 132174527 SyntenicNet32.450% 3000 medium
18equCab2 34 2,484,532,0622,428,790,173 55,741,889% 40.97 Horse6.8X 91571448 SyntenicNet34.415% 3000 medium
19cavPor3 3,144 2,723,219,6412,663,369,733 59,849,908% 27.53 Guinea pig6.76X 27942054 SyntenicNet28.447% 3000 medium
20vicPac1 298,413 2,962,253,6081,922,910,435 1,039,343,173% 32.24 Alpaca2X 230521 SyntenicNet22.636% 3000 medium
21turTru1 116,467 2,519,048,4862,298,444,090 220,604,396% 43.86 Dolphin2X 166056 SyntenicNet28.761% 3000 medium
22tupBel1 150,851 3,660,774,9572,137,225,476 1,523,549,481% 20.43 Tree shrew2X 127888 SyntenicNet19.766% 3000 medium
23susScr2 20 2,262,501,5712,231,298,548 31,203,023% 42.41 Pig24X 134541103 SyntenicNet23.248% 3000 medium
24oryCun2 3,242 2,737,490,5012,604,023,284 133,467,217% 43.74 Rabbit6.51X 111795807 SyntenicNet25.248% 3000 medium
25choHof1 481,259 2,458,927,6202,060,419,685 398,507,935% 35.67 Sloth2X 9667 SyntenicNetN/A 3000 medium
26pteVam1 96,944 1,996,076,4101,839,436,660 156,639,750% 31.75 Megabat2X 124060 SyntenicNet27.345% 3000 medium
27loxAfr3 2,353 3,196,760,8333,118,565,340 78,195,493% 47.63 Elephant7X 46401353 SyntenicNet25.823% 3000 medium
28felCat4 104,054 3,160,303,9481,990,635,005 1,169,668,943% 40.58 Cat2.8X 164876586 SyntenicNet24.033% 3000 medium
29ailMel1 81,467 2,299,509,0152,245,312,831 54,196,184% 38.96 Panda73X 1281781 SyntenicNet30.979% 3000 medium
30canFam3 3,268 2,410,976,8752,392,715,236 18,261,639% 43.01 Dog7.6X 63241923 SyntenicNet29.144% 3000 medium
31dasNov2 292,141 4,813,823,5622,371,493,872 2,442,329,690% 37.23 Armadillo2X 55360 SyntenicNet17.004% 3000 medium
32myoLuc2 11,654 2,034,575,3001,966,419,868 68,155,432% 33.71 Microbat2.18X 4293315 SyntenicNet24.363% 3000 medium
33bosTau7 11,692 2,981,119,5792,804,673,174 176,446,405% 49.56 Cow7.1X 85119472 SyntenicNet26.255% 3000 medium
34oviAri1 1,218 2,860,512,9831,201,271,277 1,659,241,706% 0.00 Sheep3X 100831284 SyntenicNet15.341% 3000 medium
35proCap1 295,006 2,985,258,9992,407,847,681 577,411,318% 28.11 Rock hyrax2X 24297 SyntenicNet15.147% 3000 medium
36ochPri2 187,558 3,445,784,3541,923,624,051 1,522,160,303% 11.44 Pika2X 88760 SyntenicNetN/A 3000 medium
37eriEur1 379,802 3,367,787,3582,133,134,836 1,234,652,522% 50.89 Hedgehog2X 33565 SyntenicNet9.856% 3000 medium
38echTel1 325,491 3,823,724,7282,111,581,369 1,712,143,359% 13.84 Tenrec2X 48377 SyntenicNet10.947% 3000 medium
39sorAra1 262,057 2,936,119,0081,832,864,697 1,103,254,311% 39.07 Shrew2X 47941 SyntenicNet9.382% 3000 medium
40macEug2 277,711 3,075,184,0242,536,076,954 539,107,070% 47.39 Wallaby2X 36602 SyntenicNet4.353% 3000 medium
41monDom5 11 3,605,631,7283,501,660,299 103,971,429% 55.95 Opossum6.8X 527952102 N/AN/A 1000 N/A
42sarHar1 35,974 3,174,693,0102,931,539,702 243,153,308% 39.66 Tasmanian devil85X 1847106 N/AN/A 1000 N/A
43 ailMis1to be done
44 croPor1to be done
45ornAna1 201,523 1,996,811,2121,842,235,522 154,575,690% 47.89 Platypus6X 991605 N/AN/A 1000 N/A
46galGal4 15,932 1,046,932,0991,032,854,810 14,077,289% 20.41 Chicken12X 90216835 N/AN/A 1000 N/A
47taeGut1 70 1,233,186,3411,222,864,691 10,321,650% 20.42 Zebra finch6X 73657157 N/AN/A 1000 N/A
48melGal1 5,891 1,061,817,101935,922,386 125,894,715% 6.60 Turkey5X 74864452 N/AN/A 1000 N/A
49 chrPic1to be done
50anoCar2 6,457 1,799,143,5871,701,353,767 97,789,820% 41.98 Lizard7.1X 150641573 N/AN/A 1000 N/A
51xenTro3 19,550 1,511,735,3261,358,334,882 153,400,444% 24.55 X. tropicalis7.65X 1567461 N/AN/A 1000 N/A
52latCha1 22,819 2,860,591,9212,183,592,768 676,999,153% 45.68 Coelacanth77.5X 924513 N/AN/A 1000 N/A
53gadMor1 427,428 824,327,835608,038,555 216,289,280% 31.25 Atlantic cod40X 393166 N/AN/A 1000 N/A
54oreNil1 5,901 927,742,539816,084,674 111,657,865% 25.51 Nile tilapia269X 2802423 N/AN/A 1000 N/A
55gasAcu1 23 463,354,448446,627,861 16,726,587% 2.58 Stickleback6X 20083130 N/AN/A 1000 N/A
56fr3 6,835 391,484,715350,961,831 40,522,884% 19.01 Fugu8.5X 11516971 N/AN/A 1000 N/A
57tetNig2 27 358,618,246302,314,788 56,303,458% 20.27 Tetraodon7.9X 13390619 N/AN/A 1000 N/A
58danRer7 1,133 1,412,464,8431,409,770,109 2,694,734% 52.06 Zebrafish30X 54093808 N/AN/A 1000 N/A
59oryLat2 7,189 869,000,216700,386,597 168,613,619% 33.09 Medaka10.6X 29908082 N/AN/A 1000 N/A
60petMar1 108,241 1,027,258,967831,696,438 195,562,529% 40.67 Lamprey5.9X 14239 N/AN/A 1000 N/A