EquCab2 Genome size statistics

see also

• Horse 6-way EquCab2 conservation alignment
• Horse 6-way EquCab2 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 equCab2 matched (chainLink table) == featureBits equCab2 chain<Db>Link == alignment coverage

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 equCab2 matched (chainLink table)	chain minScore	chain linearGap
01	equCab2	34	2,484,532,062	2,428,790,173	55,741,889	% 40.97	Horse	6.8X	91571448	N/A	N/A	1000	N/A
02	canFam2	41	2,531,673,953	2,384,996,543	146,677,410	% 40.63	Dog	7.6X	67211953	Net	70.875%	3000	medium
03	hg18	49	3,107,677,273	2,881,421,696	226,255,577	% 48.85	Human	20X	146274826	Net	66.796%	3000	medium
04	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	Net	37.150%	3000	medium
05	ornAna1	201,523	1,996,811,212	1,842,235,522	154,575,690	% 47.89	Platypus	6X	991605	Net	5.466%	5000	loose
06	galGal3	57	1,100,480,441	1,042,583,135	57,897,306	% 9.85	Chicken	6.6X	94230402	Net	3.019%	3000	medium