Ce9 Genome size statistics: Difference between revisions
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<UL> | <UL> | ||
<LI>[[ | <LI>[[Ce9 conservation alignment]]</LI> | ||
<LI>[[ | <LI>[[Ce9 conservation lastz parameters]]</LI> | ||
<LI>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
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<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 ce9 matched (chainLink table) == featureBits ce9 chain<Db>Link == alignment coverage</LI> | <LI>% of ce9 matched (chainLink table) == featureBits ce9 chain<Db>Link == alignment coverage</LI> | ||
<LI><B>NOTE:</B> stats for caeRem3 and caePb2 were collected from the scaffold/contig sequences, not the single chrUn sequence in the UCSC browser</LI> | |||
<LI><B>NOTE:</B> the 30X coverage for C. elegans is merely a place holder, the C. elegans genome is complete, I have found no estimate of coverage.</LI> | |||
<LI><B>NOTE:</B> I can find no coverage estimate for haeCon1</LI> | |||
</UL> | </UL> | ||
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<TD ALIGN=CENTER>C. elegans</TD><TH ALIGN=CENTER>30X</TH> | <TD ALIGN=CENTER>C. elegans</TD><TH ALIGN=CENTER>30X</TH> | ||
<TH ALIGN=CENTER>17493784</TH> | <TH ALIGN=CENTER>17493784</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>self alignment</TH><TD ALIGN=RIGHT>N/A</TD> | ||
<TD ALIGN=RIGHT>10000</TD> | <TD ALIGN=RIGHT>10000</TD> | ||
<TD ALIGN=CENTER>medium</TD></TR> | <TD ALIGN=CENTER>medium</TD></TR> | ||
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<TH ALIGN=RIGHT>3,670</TH> | <TH ALIGN=RIGHT>3,670</TH> | ||
<TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD> | <TD ALIGN=RIGHT>145,442,736</TD><TD ALIGN=RIGHT>138,406,203</TD> | ||
<TD ALIGN=RIGHT>7,036,533</TD><TD ALIGN=RIGHT>% | <TD ALIGN=RIGHT>7,036,533</TD><TD ALIGN=RIGHT>% 28.29</TD> | ||
<TD ALIGN=CENTER>C. remanei</TD><TH ALIGN=CENTER>9.2X</TH> | <TD ALIGN=CENTER>C. remanei</TD><TH ALIGN=CENTER>9.2X</TH> | ||
<TH ALIGN=CENTER>435512</TH> | <TH ALIGN=CENTER>435512</TH> | ||
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<TH ALIGN=RIGHT>13,589</TH> | <TH ALIGN=RIGHT>13,589</TH> | ||
<TD ALIGN=RIGHT>170,473,138</TD><TD ALIGN=RIGHT>170,473,124</TD> | <TD ALIGN=RIGHT>170,473,138</TD><TD ALIGN=RIGHT>170,473,124</TD> | ||
<TD ALIGN=RIGHT>14</TD><TD ALIGN=RIGHT>% | <TD ALIGN=RIGHT>14</TD><TD ALIGN=RIGHT>% 25.50</TD> | ||
<TD ALIGN=CENTER>C. brenneri</TD><TH ALIGN=CENTER>9.5X</TH> | <TD ALIGN=CENTER>C. brenneri</TD><TH ALIGN=CENTER>9.5X</TH> | ||
<TH ALIGN=CENTER>31774</TH> | <TH ALIGN=CENTER>31774</TH> | ||
Latest revision as of 23:46, 31 May 2011
see also
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
- NOTE: stats for caeRem3 and caePb2 were collected from the scaffold/contig sequences, not the single chrUn sequence in the UCSC browser
- NOTE: the 30X coverage for C. elegans is merely a place holder, the C. elegans genome is complete, I have found no estimate of coverage.
- NOTE: I can find no coverage estimate for haeCon1
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 | self alignment | 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 | % 28.29 | C. remanei | 9.2X | 435512 | SyntenicNet | 41.722% | 1000 | loose |
| 04 | caePb2 | 13,589 | 170,473,138 | 170,473,124 | 14 | % 25.50 | 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 |
