Ce9 Genome size statistics: Difference between revisions
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==do not edit, automatically generated table== | ==do not edit, automatically generated table== | ||
<TABLE BORDER=1> | |||
<TR><TH>order<BR>count</TH> | |||
<TH>ucsc<BR>db name</TH> | |||
<TH>chrom<BR>count</TH> | |||
<TH>total<BR>size</TH> | |||
<TH>non-N<BR>bases</TH> | |||
<TH>N base<BR>count</TH> | |||
<TH>% masked</TH> | |||
<TH>common name</TH> | |||
<TH>coverage</TH> | |||
<TH>N50<BR>chrom.sizes</TH> | |||
<TH>alignment type</TH> | |||
<TH>% of ce9<BR>matched<BR>(chainLink table)</TH> | |||
<TH>chain<BR>minScore</TH> | |||
<TH>chain<BR>linearGap</TH> | |||
<TR> | |||
<TR><TH ALIGN=RIGHT>01</TH><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/c_elegans/ ce9]</TH> | |||
<TH ALIGN=RIGHT>7</TH> | |||
<TD ALIGN=RIGHT>100,286,004</TD><TD ALIGN=RIGHT>100,286,004</TD> | |||
<TD ALIGN=RIGHT>0</TD><TD ALIGN=RIGHT>% 13.38</TD> | |||
<TD ALIGN=CENTER>C. elegans</TD><TH ALIGN=CENTER>30X</TH> | |||
<TH ALIGN=CENTER>17493784</TH> | |||
<TH ALIGN=CENTER>N/A</TH><TD ALIGN=RIGHT>N/A</TD> | |||
<TD ALIGN=RIGHT>10000</TD> | |||
<TD ALIGN=CENTER>medium</TD></TR> | |||
<TR><TH ALIGN=RIGHT>02</TH><TH ALIGN=RIGHT>[http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_briggsae/assembly/draft/Caenorhabditis_briggsae-1.0/ cb3]</TH> | |||
<TH ALIGN=RIGHT>13</TH> | |||
<TD ALIGN=RIGHT>108,492,946</TD><TD ALIGN=RIGHT>105,451,667</TD> | |||
<TD ALIGN=RIGHT>3,041,279</TD><TD ALIGN=RIGHT>% 20.11</TD> | |||
<TD ALIGN=CENTER>C. briggsae</TD><TH ALIGN=CENTER>10X</TH> | |||
<TH ALIGN=CENTER>14512975</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>42.300%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>03</TH><TH ALIGN=RIGHT>[ftp://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-15.0.1/ caeRem3]</TH> | |||
<TH ALIGN=RIGHT>3,670</TH> | |||
<TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD> | |||
<TD ALIGN=RIGHT>7,036,533</TD><TD ALIGN=RIGHT>% 0.00</TD> | |||
<TD ALIGN=CENTER>C. remanei</TD><TH ALIGN=CENTER>9.2X</TH> | |||
<TH ALIGN=CENTER>435512</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>41.722%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>04</TH><TH ALIGN=RIGHT>[ftp://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_PB2801/assembly/Caenorhabditis_PB2801-6.0.1/ caePb2]</TH> | |||
<TH ALIGN=RIGHT>13,589</TH> | |||
<TD ALIGN=RIGHT>170,473,138</TD><TD ALIGN=RIGHT>170,473,124</TD> | |||
<TD ALIGN=RIGHT>14</TD><TD ALIGN=RIGHT>% 0.00</TD> | |||
<TD ALIGN=CENTER>C. brenneri</TD><TH ALIGN=CENTER>9.5X</TH> | |||
<TH ALIGN=CENTER>31774</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>40.677%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>05</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 caeJap3]</TH> | |||
<TH ALIGN=RIGHT>35,931</TH> | |||
<TD ALIGN=RIGHT>154,057,934</TD><TD ALIGN=RIGHT>154,057,934</TD> | |||
<TD ALIGN=RIGHT>0</TD><TD ALIGN=RIGHT>% 46.67</TD> | |||
<TD ALIGN=CENTER>C. japonica</TD><TH ALIGN=CENTER>22X</TH> | |||
<TH ALIGN=CENTER>10166</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>27.580%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>06</TH><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/h_contortus/ haeCon1]</TH> | |||
<TH ALIGN=RIGHT>59,708</TH> | |||
<TD ALIGN=RIGHT>297,989,404</TD><TD ALIGN=RIGHT>278,844,984</TD> | |||
<TD ALIGN=RIGHT>19,144,420</TD><TD ALIGN=RIGHT>% 17.80</TD> | |||
<TD ALIGN=CENTER>H. contortus</TD><TH ALIGN=CENTER>1.0X</TH> | |||
<TH ALIGN=CENTER>13340</TH> | |||
<TD ALIGN=CENTER>RecipBest</TD><TD ALIGN=RIGHT>7.463%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>07</TH><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABKE priPac2]</TH> | |||
<TH ALIGN=RIGHT>13,962</TH> | |||
<TD ALIGN=RIGHT>133,635,077</TD><TD ALIGN=RIGHT>133,634,773</TD> | |||
<TD ALIGN=RIGHT>304</TD><TD ALIGN=RIGHT>% 22.63</TD> | |||
<TD ALIGN=CENTER>P. pacificus</TD><TH ALIGN=CENTER>8.92X</TH> | |||
<TH ALIGN=CENTER>18623</TH> | |||
<TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>5.862%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>08</TH><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/m_hapla/ melHap1]</TH> | |||
<TH ALIGN=RIGHT>3,452</TH> | |||
<TD ALIGN=RIGHT>53,017,507</TD><TD ALIGN=RIGHT>53,017,507</TD> | |||
<TD ALIGN=RIGHT>0</TD><TD ALIGN=RIGHT>% 52.96</TD> | |||
<TD ALIGN=CENTER>M. hapla</TD><TH ALIGN=CENTER>10.4X</TH> | |||
<TH ALIGN=CENTER>37608</TH> | |||
<TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>3.922%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>09</TH><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/m_incognita/ melInc1]</TH> | |||
<TH ALIGN=RIGHT>9,538</TH> | |||
<TD ALIGN=RIGHT>82,095,019</TD><TD ALIGN=RIGHT>82,095,019</TD> | |||
<TD ALIGN=RIGHT>0</TD><TD ALIGN=RIGHT>% 45.40</TD> | |||
<TD ALIGN=CENTER>M. incognita</TD><TH ALIGN=CENTER>5X</TH> | |||
<TH ALIGN=CENTER>12786</TH> | |||
<TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>3.301%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>10</TH><TH ALIGN=RIGHT>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS210/genomes/b_malayi/ bruMal1]</TH> | |||
<TH ALIGN=RIGHT>27,211</TH> | |||
<TD ALIGN=RIGHT>95,828,100</TD><TD ALIGN=RIGHT>89,235,536</TD> | |||
<TD ALIGN=RIGHT>6,592,564</TD><TD ALIGN=RIGHT>% 36.04</TD> | |||
<TD ALIGN=CENTER>B. malayi</TD><TH ALIGN=CENTER>9X</TH> | |||
<TH ALIGN=CENTER>37841</TH> | |||
<TH ALIGN=CENTER>Net</TH><TD ALIGN=RIGHT>4.790%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
</TABLE> | |||
Revision as of 17:51, 12 October 2010
see also
- Hg19 conservation alignment
- Hg19 conservation lastz parameters
- Hg18 44way alignment
- Hg18 44way blastz parameters
- Hg18 genome size statistics
- Marmoset calJac3 13-way size statistics
statistics collected from UCSC 2bit files
- The external links from the UCSC database name go to the sequencing center information pages for this 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 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
- % masked == masked either with WindowMasker or RepeatMasker plus TRF simple repeats
- % of ce9 matched (chainLink table) == featureBits ce9 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 | coverage | N50 chrom.sizes |
alignment type | % of ce9 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | ce9 | 7 | 100,286,004 | 100,286,004 | 0 | % 13.38 | C. elegans | 30X | 17493784 | N/A | N/A | 10000 | medium |
| 02 | cb3 | 13 | 108,492,946 | 105,451,667 | 3,041,279 | % 20.11 | C. briggsae | 10X | 14512975 | SyntenicNet | 42.300% | 1000 | loose |
| 03 | caeRem3 | 3,670 | 145,442,736 | 138,406,203 | 7,036,533 | % 0.00 | C. remanei | 9.2X | 435512 | SyntenicNet | 41.722% | 1000 | loose |
| 04 | caePb2 | 13,589 | 170,473,138 | 170,473,124 | 14 | % 0.00 | C. brenneri | 9.5X | 31774 | SyntenicNet | 40.677% | 1000 | loose |
| 05 | caeJap3 | 35,931 | 154,057,934 | 154,057,934 | 0 | % 46.67 | C. japonica | 22X | 10166 | SyntenicNet | 27.580% | 1000 | loose |
| 06 | haeCon1 | 59,708 | 297,989,404 | 278,844,984 | 19,144,420 | % 17.80 | H. contortus | 1.0X | 13340 | RecipBest | 7.463% | 1000 | loose |
| 07 | priPac2 | 13,962 | 133,635,077 | 133,634,773 | 304 | % 22.63 | P. pacificus | 8.92X | 18623 | Net | 5.862% | 1000 | loose |
| 08 | melHap1 | 3,452 | 53,017,507 | 53,017,507 | 0 | % 52.96 | M. hapla | 10.4X | 37608 | Net | 3.922% | 1000 | loose |
| 09 | melInc1 | 9,538 | 82,095,019 | 82,095,019 | 0 | % 45.40 | M. incognita | 5X | 12786 | Net | 3.301% | 1000 | loose |
| 10 | bruMal1 | 27,211 | 95,828,100 | 89,235,536 | 6,592,564 | % 36.04 | B. malayi | 9X | 37841 | Net | 4.790% | 1000 | loose |
