Fr3 Genome size statistics

see also

• Fugu 6-way Fr3 conservation alignment
• Fugu 6-way Fr3 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 fr3 matched (chainLink table)	chain minScore	chain linearGap
01	fr3	6,835	391,484,715	350,961,831	40,522,884	% 19.01	Fugu	8.5X	11516971	N/A	N/A	N/A	N/A
02	tetNig2	27	358,618,246	302,314,788	56,303,458	% 20.27	Tetraodon	7.9X	13390619	Net	70.912%	2000	medium
03	oreNil1	5,901	927,742,539	816,084,674	111,657,865	% 25.51	Nile tilapia	269X	2802423	Net	57.240%	2000	medium
04	gasAcu1	23	463,354,448	446,627,861	16,726,587	% 2.58	Stickleback	6X	20083130	Net	55.527%	2000	medium
05	gadMor1	427,428	824,327,835	608,038,555	216,289,280	% 31.25	Atlantic cod	40X	393166	Net	30.327%	2000	medium
06	oryLat2	7,189	869,000,216	700,386,597	168,613,619	% 33.09	Medaka	10.6X	29908082	Net	43.863%	2000	medium
07	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	Net	22.823%	2000	medium
08	latCha1	22,819	2,860,591,921	2,183,592,768	676,999,153	% 45.68	Coelacanth	77.5X	924513	Net	13.735%	2000	medium