PanTro3 Genome size statistics

• PanTro3 conservation lastz parameters
• PanTro3 conservation alignment
• Hg19 conservation alignment
• Hg19 conservation lastz parameters
• Hg18 44way alignment
• Hg18 44way blastz parameters
• Hg18 genome size statistics
• Marmoset calJac3 13-way size statistics

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 hg19 matched (chainLink table) == featureBits hg19 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 panTro3 matched (chainLink table)	chain minScore	chain linearGap
01	panTro3	24,132	3,307,960,432	2,900,529,764	407,430,668	% 50.64	Chimp	6X	143986469	N/A	N/A	1000	N/A
02	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	SynetnicNet	95.597%	5000	medium
03	ponAbe2	55	3,446,771,396	3,093,543,172	353,228,224	% 50.89	Orangutan	6X	135191526	SyntenicNet	89.586%	5000	medium
04	rheMac2	22	2,864,106,071	2,646,668,809	217,437,262	% 48.28	Rhesus	5.1X	153947521	SyntenicNet	81.342%	5000	medium
05	calJac3	14,205	2,914,958,544	2,752,505,800	162,452,744	% 47.71	Marmoset	6X	132174527	SyntenicNet	69.662%	5000	medium
06	equCab2	34	2,484,532,062	2,428,790,173	55,741,889	% 40.97	Horse	6.8X	91571448	SyntenicNet	56.504%	3000	medium
07	canFam2	41	2,531,673,953	2,384,996,543	146,677,410	% 40.63	Dog	7.6X	67211953	SyntenicNet	51.588%	3000	medium
08	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	SyntenicNet	32.044%	3000	medium
09	rn4	45	2,834,127,293	2,566,294,765	267,832,528	% 44.29	Rat	20X	143002779	SyntenicNet	30.350%	3000	medium
10	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	SyntenicNet	13.743%	5000	loose
11	galGal3	57	1,100,480,441	1,042,583,135	57,897,306	% 9.85	Chicken	6.6X	94230402	SyntenicNet	4.557%	5000	loose
12	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	SyntenicNet	2.558%	5000	loose