DanRer10 12-way Genome size statistics

see also

• Zebrafish 12-way DanRer10 12-way conservation alignment
• Zebrafish 12-way DanRer10 12-way 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-preview 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 danRer10 matched (chainLink table)	chain minScore	chain linearGap
01	danRer10	1,061	1,371,719,383	1,369,631,918	2,087,465	% 52.32	Zebrafish	30X	53345113	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	Net	9.814%	2000	medium
03	lepOcu1	1,925	945,874,548	869,414,359	76,460,189	% 24.85	Spotted gar	677.5X	50348508	Net	8.409%	5000	loose
04	tetNig2	27	358,618,246	302,314,788	56,303,458	% 20.27	Tetraodon	7.9X	13390619	Net	6.063%	2000	medium
05	fr3	6,835	391,484,715	350,961,831	40,522,884	% 19.01	Fugu	8.5X	11516971	Net	7.080%	2000	medium
06	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	Net	9.640%	2000	medium
07	xenTro9	6,822	1,440,398,454	1,369,865,365	70,533,089	% 34.42	X. tropicalis	7.6X	135134832	Net	6.731%	5000	loose
08	galGal6	464	1,065,365,425	1,055,580,959	9,784,466	% 21.41	Chicken	82X	91315245	Net	5.871%	1000	loose
09	calMil1	21,204	974,498,586	936,953,443	37,545,143	% 28.08	Elephant shark	19.25X	4521921	Net	5.599%	5000	loose
10	hg38	640	3,272,116,950	3,110,748,256	161,368,694	% 52.11	Human	20X	145138636	Net	7.110%	5000	loose
11	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	Net	5.228%	5000	loose
12	latCha1	22,819	2,860,591,921	2,183,592,768	676,999,153	% 45.68	Coelacanth	77.5X	924513	Net	6.319%	5000	loose