Ce9 Genome size statistics

see also

• Ce9 conservation alignment
• Ce9 conservation lastz parameters
• all other UCSC Multiple Alignments

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