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>


==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&nbsp;name</TH>
  <TH>chrom<BR>count</TH>
  <TH>total<BR>size</TH>
  <TH>non-N<BR>bases</TH>
  <TH>N&nbsp;base<BR>count</TH>
  <TH>%&nbsp;masked</TH>
  <TH>common&nbsp;name</TH>
  <TH>coverage</TH>
  <TH>N50<BR>chrom.sizes</TH>
  <TH>alignment&nbsp;type</TH>
  <TH>%&nbsp;of&nbsp;ce9<BR>matched<BR>(chainLink&nbsp;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>%&nbsp;13.38</TD>
  <TD ALIGN=CENTER>C. elegans</TD><TH ALIGN=CENTER>30X</TH>
<TH ALIGN=CENTER>17493784</TH>
  <TH ALIGN=CENTER>self alignment</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>%&nbsp;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>%&nbsp;28.29</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>%&nbsp;25.50</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>%&nbsp;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>%&nbsp;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>%&nbsp;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>%&nbsp;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>%&nbsp;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>%&nbsp;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>

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
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