XenTro3 Genome size statistics

see also

• X. tropicalis 9-way XenTro3 conservation alignment
• X. tropicalis 9-way XenTro3 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-test 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-test	chrom count	total size	non-N bases	N base count	% masked	common name/ src info	coverage	N50 chrom.sizes	alignment type	% of xenTro3 matched (chainLink table)	chain minScore	chain linearGap
01	xenTro3	19,550	1,511,735,326	1,358,334,882	153,400,444	% 24.55	X. tropicalis	7.65X	1567461	N/A	N/A	N/A	N/A
02	anoCar2	6,457	1,799,143,587	1,701,353,767	97,789,820	% 41.98	Lizard	7.1X	150641573	Net	6.775%	5000	loose
03	galGal3	57	1,100,480,441	1,042,583,135	57,897,306	% 9.85	Chicken	6.6X	94230402	Net	4.730%	5000	loose
04	melGal1	5,891	1,061,817,101	935,922,386	125,894,715	% 6.00	Turkey	5X	74864452	Net	4.203%	5000	loose
05	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	Net	5.492%	5000	loose
06	rn4	45	2,834,127,293	2,566,294,765	267,832,528	% 44.29	Rat	20X	143002779	Net	5.216%	5000	loose
07	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	Net	6.609%	5000	loose
08	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	Net	6.694%	5000	loose
09	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	Net	7.107%	5000	loose