Rn6 20-way Genome size statistics

see also

• Rat 20-way Rn6 20-way conservation alignment
• Rat 20-way Rn6 20-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-preview 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-preview	chrom count	total size	non-N bases	N base count	% masked	common name/ src info	coverage	N50 chrom.sizes	alignment type	% of rn6 matched (chainLink table)	chain minScore	chain linearGap
01	rn6	953	2,870,182,909	2,729,860,805	140,322,104	% 43.31	Rat	10X	145729302	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	71.015%	5000	medium
03	micOch1	6,335	2,287,340,943	2,104,321,675	183,019,268	% 23.89	Prairie vole	94X	61813736	SyntenicNet	57.205%	3000	medium
04	cavPor3	3,144	2,723,219,641	2,663,369,733	59,849,908	% 27.53	Guinea pig	6.76X	27942054	SyntenicNet	27.834%	3000	medium
05	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	SyntenicNet	34.899%	3000	medium
06	panTro5	44,449	3,231,170,666	3,132,619,616	98,551,050	% 52.72	Chimp	6X	135926727	SyntenicNet	40.816%	3000	medium
07	tarSyr2	337,189	3,453,864,774	3,405,755,564	48,109,210	% 47.85	Tarsier	48X	401181	RecipBest	38.509%	3000	medium
08	rheMac8	284,728	3,236,224,332	3,142,091,753	94,132,579	% 54.33	Rhesus	47.4X	144306982	SyntenicNet	40.165%	3000	medium
09	canFam3	3,268	2,410,976,875	2,392,715,236	18,261,639	% 43.01	Dog	7.6X	63241923	SyntenicNet	28.540%	3000	medium
10	oryCun2	3,242	2,737,490,501	2,604,023,284	133,467,217	% 43.74	Rabbit	6.51X	111795807	SyntenicNet	24.654%	3000	medium
11	felCat8	267,625	2,641,342,258	2,599,700,169	41,642,089	% 44.41	Cat	20X	142431058	SyntenicNet	29.520%	3000	medium
12	ailMel1	81,467	2,299,509,015	2,245,312,831	54,196,184	% 38.96	Panda	73X	1281781	RecipBest	30.404%	3000	medium
13	bosTau8	3,179	2,670,044,500	2,649,304,231	20,740,269	% 48.69	Cow	9X	105708250	SyntenicNet	25.902%	3000	medium
14	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	SyntenicNet	9.652%	5000	loose
15	ornAna2	201,525	1,996,826,513	1,842,250,823	154,575,690	% 48.56	Platypus	6X	991605	Net	6.389%	5000	loose
16	xenTro7	7,728	1,437,530,879	1,365,936,747	71,594,132	% 33.98	X. tropicalis	7.44X	124127367	Net	4.104%	5000	loose
17	galGal5	23,475	1,230,258,557	1,218,492,533	11,766,024	% 25.74	Chicken	70X	82310166	Net	3.983%	5000	loose
18	melGal5	231,286	1,128,339,136	1,093,044,709	35,294,427	% 22.09	Turkey	35X	59006440	Net	2.440%	5000	loose
19	calMil1	21,204	974,498,586	936,953,443	37,545,143	% 28.08	Elephant shark	19.25X	4521921	Net	1.664%	5000	loose
20	danRer10	1,061	1,371,719,383	1,369,631,918	2,087,465	% 52.32	Zebrafish	30X	53345113	Net	3.232%	5000	loose