PetMar1 Genome size statistics

see also

• Lamprey 6-way PetMar1 conservation alignment
• Lamprey 6-way PetMar1 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 petMar1 matched (chainLink table)	chain minScore	chain linearGap
01	petMar1	108,241	1,027,258,967	831,696,438	195,562,529	% 40.67	Lamprey	5.9X	14239	N/A	N/A	N/A	N/A
02	galGal3	57	1,100,480,441	1,042,583,135	57,897,306	% 9.85	Chicken	6.6X	94230402	Net	2.682%	5000	loose
03	hg18	49	3,107,677,273	2,881,421,696	226,255,577	% 48.85	Human	20X	146274826	Net	3.216%	5000	loose
04	mm9	35	2,725,765,481	2,620,345,972	105,419,509	% 44.09	Mouse	20X	131738871	Net	3.132%	5000	loose
05	oryLat1	26	843,500,808	700,386,597	143,114,211	% 33.05	Medaka	10.6X	31848461	Net	2.809%	3000	medium
06	braFlo1	2	926,386,587	831,202,022	95,184,565	% 26.41	Lancelet	11.5X	926371504	Net	3.291%	5000	loose