Ce9 Genome size statistics: Difference between revisions

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<UL>
<UL>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Ce9 conservation alignment]]</LI>
<LI>[[Hg19 conservation lastz parameters]]</LI>
<LI>[[Ce9 conservation lastz parameters]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 genome size statistics]]</LI>
<LI>[[Marmoset calJac3 13-way size statistics]]</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>N/A</TH><TD ALIGN=RIGHT>N/A</TD>
   <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>%&nbsp;0.00</TD>
   <TD ALIGN=RIGHT>7,036,533</TD><TD ALIGN=RIGHT>%&nbsp;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>%&nbsp;0.00</TD>
   <TD ALIGN=RIGHT>14</TD><TD ALIGN=RIGHT>%&nbsp;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
01ce9 7 100,286,004100,286,004 0% 13.38 C. elegans30X 17493784 self alignmentN/A 10000 medium
02cb3 13 108,492,946105,451,667 3,041,279% 20.11 C. briggsae10X 14512975 SyntenicNet42.300% 1000 loose
03caeRem3 3,670 145,442,736138,406,203 7,036,533% 28.29 C. remanei9.2X 435512 SyntenicNet41.722% 1000 loose
04caePb2 13,589 170,473,138170,473,124 14% 25.50 C. brenneri9.5X 31774 SyntenicNet40.677% 1000 loose
05caeJap3 35,931 154,057,934154,057,934 0% 46.67 C. japonica22X 10166 SyntenicNet27.580% 1000 loose
06haeCon1 59,708 297,989,404278,844,984 19,144,420% 17.80 H. contortus1.0X 13340 RecipBest7.463% 1000 loose
07priPac2 13,962 133,635,077133,634,773 304% 22.63 P. pacificus8.92X 18623 Net5.862% 1000 loose
08melHap1 3,452 53,017,50753,017,507 0% 52.96 M. hapla10.4X 37608 Net3.922% 1000 loose
09melInc1 9,538 82,095,01982,095,019 0% 45.40 M. incognita5X 12786 Net3.301% 1000 loose
10bruMal1 27,211 95,828,10089,235,536 6,592,564% 36.04 B. malayi9X 37841 Net4.790% 1000 loose