Mm39 35-way Genome size statistics

see also

• Mouse 35-way Mm39 35-way conservation alignment
• Mouse 35-way Mm39 35-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 mm39 matched (chainLink table)	chain minScore	chain linearGap
01	mm39	61	2,728,222,451	2,654,621,783	73,600,668	% 45.00	Mouse	20X	130530862	N/A	N/A	N/A	N/A
02	rn6	953	2,870,182,909	2,729,860,805	140,322,104	% 43.31	Rat	10X	145729302	SyntenicNet	70.901%	5000	medium
03	GCF_003668045.3	647	2,366,634,374	2,364,208,470	2,425,904	% 31.58	Cricetulus griseus	31X	1294537483	SyntenicNet	58.000%	3000	medium
04	casCan1	21,157	2,518,306,565	2,517,974,654	331,911	% 32.86	Beaver	110X	317708	RecipBest	36.600%	3000	medium
05	speTri2	12,483	2,478,393,770	2,311,060,300	167,333,470	% 36.27	Squirrel	495X	8192786	RecipBest	34.147%	3000	medium
06	manPen1	92,770	2,204,741,241	1,998,946,804	205,794,437	% 32.83	Chinese pangolin	61X	117920	RecipBest	27.322%	3000	medium
07	cavPor3	3,144	2,723,219,641	2,663,369,733	59,849,908	% 27.53	Guinea pig	6.76X	27942054	SyntenicNet	28.378%	3000	medium
08	galVar1	179,514	3,187,660,572	2,802,837,430	384,823,142	% 38.66	Malayan flying lemur	55X	245189	Net	35.714%	3000	medium
09	calJac4	964	2,897,824,427	2,859,816,984	38,007,443	% 49.16	Marmoset	40X	137671225	SyntenicNet	33.090%	3000	medium
10	gorGor6	5,486	3,044,872,214	2,999,027,915	45,844,299	% 50.29	Gorilla	66.9X	127988552	SyntenicNet	35.064%	3000	medium
11	hg38	640	3,272,116,950	3,110,748,256	161,368,694	% 52.11	Human	20X	145138636	SyntenicNet	35.372%	3000	medium
12	panPan3	4,293	3,051,901,337	3,015,350,297	36,551,040	% 50.21	Bonobo	74X	129867894	SyntenicNet	35.282%	3000	medium
13	panTro6	4,346	3,050,398,082	3,018,592,990	31,805,092	% 53.55	Chimp	124X	130782606	SyntenicNet	35.291%	3000	medium
14	tarSyr2	337,189	3,453,864,774	3,405,755,564	48,109,210	% 47.85	Tarsier	48X	401181	RecipBest	32.278%	3000	medium
15	rheMac10	2,939	2,971,331,530	2,936,892,725	34,438,805	% 52.41	Rhesus	50X	145679320	SyntenicNet	34.838%	3000	medium
16	otoGar3	7,793	2,519,724,550	2,359,530,453	160,194,097	% 39.51	Bushbaby	137X	13852661	RecipBest	29.729%	3000	medium
17	equCab3	4,701	2,506,966,135	2,497,530,654	9,435,481	% 44.49	Horse	88X	87230776	SyntenicNet	34.831%	3000	medium
18	turTru2	240,901	2,551,996,573	2,332,402,443	219,594,130	% 43.56	Dolphin	3.5X	116261	RecipBest	30.188%	3000	medium
19	canFam4	2,198	2,482,000,080	2,481,941,580	58,500	% 43.54	Dog	100X	64299765	SyntenicNet	29.376%	3000	medium
20	tupBel1	150,851	3,660,774,957	2,137,225,476	1,523,549,481	% 20.43	Tree shrew	2X	127888	RecipBest	19.691%	3000	medium
21	susScr3	4,583	2,808,525,991	2,518,987,191	289,538,800	% 44.30	Pig	24X	148491826	RecipBest	25.611%	3000	medium
22	loxAfr3	2,353	3,196,760,833	3,118,565,340	78,195,493	% 47.63	Elephant	7X	46401353	RecipBest	25.756%	3000	medium
23	oryCun2	3,242	2,737,490,501	2,604,023,284	133,467,217	% 43.74	Rabbit	6.51X	111795807	RecipBest	25.182%	3000	medium
24	oviAri4	5,466	2,615,516,299	2,587,507,373	28,008,926	% 45.81	Sheep	166X	100009711	SyntenicNet	26.200%	3000	medium
25	neoSch1	7,872	2,400,839,308	2,347,122,535	53,716,773	% 43.31	Hawaiian monk seal	61X	29518589	SyntenicNet	31.257%	3000	medium
26	bosTau9	2,211	2,715,853,792	2,715,825,630	28,162	% 49.35	Cow	80X	103308737	RecipBest	26.588%	3000	medium
27	ochPri3	10,420	2,229,835,716	1,943,987,870	285,847,846	% 29.53	Pika	103X	26863993	RecipBest	18.559%	3000	medium
28	eriEur2	5,803	2,715,720,925	2,333,073,535	382,647,390	% 45.60	Hedgehog	79X	3264618	RecipBest	13.450%	3000	medium
29	echTel2	8,402	2,947,024,286	2,605,196,361	341,827,925	% 28.26	Tenrec	78X	45764842	RecipBest	14.456%	3000	medium
30	sorAra2	12,845	2,423,158,183	2,192,103,426	231,054,757	% 32.76	Shrew	120X	22794405	RecipBest	13.370%	3000	medium
31	monDom5	11	3,605,631,728	3,501,660,299	103,971,429	% 55.95	Opossum	6.8X	527952102	Net	5.382%	5000	loose
32	xenTro9	6,822	1,440,398,454	1,369,865,365	70,533,089	% 34.42	X. tropicalis	7.6X	135134832	Net	1.936%	5000	loose
33	galGal6	464	1,065,365,425	1,055,580,959	9,784,466	% 21.41	Chicken	82X	91315245	Net	2.537%	5000	loose
34	petMar3	12,062	1,130,433,897	1,043,181,598	87,252,299	% 45.11	Lamprey	100X	11932523	Net	0.905%	5000	loose
35	danRer11	1,923	1,679,203,469	1,674,509,851	4,693,618	% 51.76	Zebrafish	30X	52186027	Net	1.416%	5000	loose