Marmoset calJac3 13-way size statistics

see also

• Marmoset 13-way CalJac3 conservation alignment
• Marmoset 13-way CalJac3 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 calJac3 matched (chainLink table) == featureBits calJac3 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 calJac3 matched (chainLink table)	chain minScore	chain linearGap
01	calJac3	14,205	2,914,958,544	2,752,505,800	162,452,744	% 47.71	Marmoset	6X	132174527	N/A	N/A	N/A	N/A
02	ponAbe2	55	3,446,771,396	3,093,543,172	353,228,224	% 50.89	Orangutan	6X	135191526	SyntenicNet	71.893%	5000	medium
03	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	SyntenicNet	73.768%	5000	medium
04	panTro2	52	3,350,447,512	2,909,246,738	441,200,774	% 48.90	Chimp	6X	145085868	SyntenicNet	72.304%	5000	medium
05	gorGor2	58,049	3,035,791,622	2,829,687,208	206,104,414	% 48.19	Gorilla	2X	913458	RecipBest	76.343%	3000	medium
06	rheMac2	22	2,864,106,071	2,646,668,809	217,437,262	% 48.28	Rhesus	5.1X	153947521	SyntenicNet	69.625%	5000	medium
07	papHam1	387,374	2,867,564,654	2,741,849,051	125,715,603	% 48.70	Baboon	5.3X	88525	RecipBest	70.053%	5000	medium
08	tarSyr1	656,709	3,179,905,132	2,768,536,343	411,368,789	% 41.75	Tarsier	2X	12214	RecipBest	46.729%	3000	medium
09	micMur1	185,042	2,902,270,736	1,852,394,361	1,049,876,375	% 37.31	Mouse lemur	2X	140884	RecipBest	45.726%	3000	medium
10	otoGar1	120,882	3,420,058,864	1,969,052,059	1,451,006,805	% 34.89	Bushbaby	2X	139426	RecipBest	42.743%	3000	medium
11	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	SyntenicNet	31.310%	3000	medium
12	canFam2	41	2,531,673,953	2,384,996,543	146,677,410	% 40.63	Dog	7.6X	67211953	SyntenicNet	50.766%	3000	medium
13	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	SyntenicNet	7.906%	5000	loose