PetMar2 Genome size statistics

see also

• Lamprey 7-way PetMar2 conservation alignment
• Lamprey 7-way PetMar2 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 petMar2 matched (chainLink table)	chain minScore	chain linearGap
01	petMar2	25,006	885,550,958	647,368,134	238,182,824	% 42.47	Lamprey	5.0X	184619	N/A	N/A	N/A	N/A
02	galGal4	15,932	1,046,932,099	1,032,854,810	14,077,289	% 20.41	Chicken	12X	90216835	Net	2.869%	5000	loose
03	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	Net	4.926%	5000	loose
04	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	Net	2.618%	5000	loose
05	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	Net	3.324%	5000	loose
06	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	Net	3.232%	5000	loose
07	braFlo2	399	521,910,208	480,418,582	41,491,626	% 25.49	Lancelet	11.5X	2586727	Net	3.020%	5000	loose