Ce9 Genome size statistics: Difference between revisions

Latest revision as of 23:46, 31 May 2011

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

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

@@ Line 4: / Line 4: @@
 <LI>[[Ce9 conservation alignment]]</LI>
 <LI>[[Ce9 conservation lastz parameters]]</LI>
-<LI>[[Hg19 conservation alignment]]</LI>
+<LI>all other [[UCSC Multiple Alignments]]</LI>
-<LI>[[Hg19 conservation lastz parameters]]</LI>
-<LI>[[Hg18 44way alignment]]</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>
@@ Line 66: / Line 61: @@
 <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;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>
 <TH ALIGN=CENTER>435512</TH>
@@ Line 75: / Line 70: @@
 <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;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>
 <TH ALIGN=CENTER>31774</TH>