Ce10 Genome size statistics

see also

• June 2011 C. elegans 9-way Ce10 conservation alignment
• June 2011 C. elegans 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-preview	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