DanRer7 Genome size statistics

see also

• Zebrafish 8-way DanRer7 conservation alignment
• Zebrafish 8-way DanRer7 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 danRer7 matched (chainLink table) == featureBits danRer7 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 danRer7 matched (chainLink table)	chain minScore	chain linearGap
01	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	N/A	N/A	N/A	N/A
02	gasAcu1	23	463,354,448	446,627,861	16,726,587	% 2.58	Stickleback	6X	20083130	MAF net	10.270%	2000	medium
03	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	MAF net	10.032%	2000	medium
04	tetNig2	27	358,618,246	302,314,788	56,303,458	% 20.27	Tetraodon	7.9X	13390619	MAF net	6.273%	2000	medium
05	fr2	2	400,525,790	351,212,245	49,313,545	% 19.01	Fugu	8.5X	400509343	MAF net	7.363%	2000	medium
06	xenTro2	19,759	1,513,925,492	1,359,400,017	154,525,475	% 19.65	X. tropicalis	7.65X	1564123	MAF net	6.428%	5000	loose
07	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	MAF net	5.104%	5000	loose
08	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	MAF net	6.151%	5000	loose