GeoFor1 Genome size statistics

see also

• Medium ground finch 7-way GeoFor1 conservation alignment
• Medium ground finch 7-way GeoFor1 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 geoFor1 matched (chainLink table)	chain minScore	chain linearGap
01	geoFor1	27,239	1,065,292,181	1,041,286,029	24,006,152	% 19.99	Medium ground finch	115X	5255844	N/A	N/A	N/A	N/A
02	taeGut1	70	1,233,186,341	1,222,864,691	10,321,650	% 20.42	Zebra finch	6X	73657157	SyntenicNet	92.532%	1000	loose
03	melUnd1	25,212	1,117,373,619	1,086,614,815	30,758,804	% 19.62	Budgerigar	7X	10614383	SyntenicNet	80.650%	1000	loose
04	galGal4	15,932	1,046,932,099	1,032,854,810	14,077,289	% 20.41	Chicken	12X	90216835	SyntenicNet	70.718%	1000	loose
05	melGal1	5,891	1,061,817,101	935,922,386	125,894,715	% 6.60	Turkey	5X	74864452	SyntenicNet	67.079%	1000	loose
06	hg19	93	3,137,161,264	2,897,310,462	239,850,802	% 50.63	Human	20X	146364022	RecipBest	8.504%	5000	loose
07	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	RecipBest	7.709%	5000	loose