XenTro9 11-way Genome size statistics

see also

• X. tropicalis 11-way XenTro9 11-way conservation alignment
• X. tropicalis 11-way XenTro9 11-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 xenTro9 matched (chainLink table)	chain minScore	chain linearGap
01	xenTro9	6,822	1,440,398,454	1,369,865,365	70,533,089	% 34.42	X. tropicalis	7.6X	135134832	N/A	N/A	N/A	N/A
02	xenLae2	108,033	2,718,433,805	2,408,724,787	309,709,018	% 40.59	African clawed frog	30X	136570856	SyntenicNet	54.877%	1000	loose
03	nanPar1	25,187	2,053,849,526	1,977,771,384	76,078,142	% 38.90	Tibetan frog	83X	1069101	RecipBest	8.180%	1000	loose
04	chrPic2	78,595	2,365,766,562	2,173,204,089	192,562,473	% 31.52	Painted turtle	15X	7072151	RecipBest	6.459%	5000	loose
05	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	SyntenicNet	5.414%	5000	loose
06	galGal5	23,475	1,230,258,557	1,218,492,533	11,766,024	% 25.74	Chicken	70X	82310166	SyntenicNet	3.387%	1000	loose
07	anoCar2	6,457	1,799,143,587	1,701,353,767	97,789,820	% 41.98	Lizard	7.1X	150641573	SyntenicNet	5.977%	5000	loose
08	canFam3	3,268	2,410,976,875	2,392,715,236	18,261,639	% 43.01	Dog	7.6X	63241923	SyntenicNet	3.311%	5000	loose
09	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	SyntenicNet	7.950%	5000	loose
10	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	SyntenicNet	6.581%	5000	loose
11	fr3	6,835	391,484,715	350,961,831	40,522,884	% 19.01	Fugu	8.5X	11516971	SyntenicNet	3.777%	5000	loose