Ce10 Genome size statistics: Difference between revisions
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(updated N50 numbers) |
(fixup links to external source sequence) |
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==do not edit, automatically generated table== | ==do not edit, automatically generated table== | ||
<TABLE BORDER=1> | <TABLE BORDER=1> | ||
<TR><TH>order<BR>count/<BR>ftp src</TH> | <TR><TH>order<BR>count/<BR>ftp src</TH> | ||
<TH>ucsc<BR>db name/<BR> | <TH>ucsc<BR>db name/<BR>genome-test</TH> | ||
<TH>chrom<BR>count</TH> | <TH>chrom<BR>count</TH> | ||
<TH>total<BR>size</TH> | <TH>total<BR>size</TH> | ||
| Line 30: | Line 31: | ||
<TH>N base<BR>count</TH> | <TH>N base<BR>count</TH> | ||
<TH>% masked</TH> | <TH>% masked</TH> | ||
<TH>common name/<BR> | <TH>common name/<BR>src info</TH> | ||
<TH>coverage</TH> | <TH>coverage</TH> | ||
<TH>N50<BR>chrom.sizes</TH> | <TH>N50<BR>chrom.sizes</TH> | ||
| Line 83: | Line 84: | ||
<TD ALIGN=RIGHT>1000</TD> | <TD ALIGN=RIGHT>1000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp. | <TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ 06]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH> | ||
<TH ALIGN=RIGHT>3,307</TH> | <TH ALIGN=RIGHT>3,307</TH> | ||
<TD ALIGN=RIGHT>190,374,847</TD><TD ALIGN=RIGHT>170,097,428</TD> | <TD ALIGN=RIGHT>190,374,847</TD><TD ALIGN=RIGHT>170,097,428</TD> | ||
| Line 101: | Line 102: | ||
<TD ALIGN=RIGHT>1000</TD> | <TD ALIGN=RIGHT>1000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp. | <TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ 08]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH> | ||
<TH ALIGN=RIGHT>18,817</TH> | <TH ALIGN=RIGHT>18,817</TH> | ||
<TD ALIGN=RIGHT>166,256,191</TD><TD ALIGN=RIGHT>154,057,934</TD> | <TD ALIGN=RIGHT>166,256,191</TD><TD ALIGN=RIGHT>154,057,934</TD> | ||
Revision as of 23:30, 8 June 2011
see also
- June 2011 9-way Ce10 conservation alignment
- June 2011 9-way Ce10_conservation_lastz_parameters
- all other UCSC Multiple Alignments
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 ce10 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | ce10 | 7 | 100,286,070 | 100,286,070 | 0 | % 13.38 | C. elegans | 30X | 17493793 | N/A | N/A | 1000 | N/A |
| 02 | cb4 | 13 | 108,434,085 | 105,430,959 | 3,003,126 | % 36.52 | C. briggsae | 10X | 17485439 | SyntenicNet | 39.386% | 1000 | loose |
| 03 | caeSp91 | 7,636 | 204,396,809 | 186,540,270 | 17,856,539 | % 31.67 | C. sp. 9 ju1422 | 37.6X | 196652 | SyntenicNet | 42.169% | 1000 | loose |
| 04 | caeRem4 | 3,670 | 145,442,736 | 138,406,203 | 7,036,533 | % 30.48 | C. remanei | 9.2X | 435512 | SyntenicNet | 41.722% | 1000 | loose |
| 05 | caeSp111 | 665 | 79,321,433 | 76,497,192 | 2,824,241 | % 29.15 | C. sp. 11 ju1373 | 20.2X | 20921866 | SyntenicNet | 37.876% | 1000 | loose |
| 06 | caePb3 | 3,307 | 190,374,847 | 170,097,428 | 20,277,419 | % 29.30 | C. brenneri | 9.5X | 381961 | SyntenicNet | 40.644% | 1000 | loose |
| 07 | caeSp71 | 52,546 | 196,410,749 | 177,605,791 | 18,804,958 | % 31.53 | C. sp. 7 ju1286 | 37.9X | 73785 | SyntenicNet | 40.236% | 1000 | loose |
| 08 | caeJap4 | 18,817 | 166,256,191 | 154,057,934 | 12,198,257 | % 46.77 | C. japonica | 22X | 94149 | SyntenicNet | 27.737% | 1000 | loose |
| 09 | caeAng1 | 33,559 | 79,761,545 | 75,258,781 | 4,502,764 | % 38.31 | C. angaria | 170X | 9453 | SyntenicNet | 17.625% | 1000 | loose |
