Rn5 13-way Genome size statistics

see also

• Rat 13-way Rn5 13-way conservation alignment
• Rat 13-way Rn5 13-way 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 rn5 matched (chainLink table)	chain minScore	chain linearGap
01	rn5	2,739	2,909,698,938	2,572,853,723	336,845,215	% 42.81	Rat	6X	154597545	N/A	N/A	N/A	N/A
02	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	SyntenicNet	70.278%	5000	medium
03	cavPor3	3,144	2,723,219,641	2,663,369,733	59,849,908	% 27.53	Guinea pig	6.76X	27942054	SyntenicNet	29.127%	3000	medium
04	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	SyntenicNet	36.312%	3000	medium
05	panTro4	24,129	3,309,577,922	2,902,338,967	407,238,955	% 51.29	Chimp	6X	143986469	SyntenicNet	35.616%	3000	medium
06	rheMac3	34,103	2,969,988,180	2,639,145,830	330,842,350	% 48.54	Rhesus	50X	150158102	SyntenicNet	34.835%	3000	medium
07	canFam3	3,268	2,410,976,875	2,392,715,236	18,261,639	% 43.01	Dog	7.6X	63241923	SyntenicNet	29.852%	3000	medium
08	ailMel1	81,467	2,299,509,015	2,245,312,831	54,196,184	% 38.96	Panda	73X	1281781	RecipBest	31.818%	3000	medium
09	bosTau7	11,692	2,981,119,579	2,804,673,174	176,446,405	% 49.56	Cow	7.1X	85119472	SyntenicNet	26.820%	3000	medium
10	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	Net	9.694%	5000	loose
11	galGal4	15,932	1,046,932,099	1,032,854,810	14,077,289	% 20.41	Chicken	12X	90216835	Net	3.788%	5000	loose
12	melGal1	5,891	1,061,817,101	935,922,386	125,894,715	% 6.60	Turkey	5X	74864452	Net	3.630%	5000	loose
13	danRer7	1,133	1,412,464,843	1,409,770,109	2,694,734	% 52.06	Zebrafish	30X	54093808	Net	2.588%	5000	loose