Hg38 17-way Genome size statistics

see also

• Human 17-way Hg38 17-way conservation alignment
• Human 17-way Hg38 17-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 hg38 matched (chainLink table)	chain minScore	chain linearGap
01	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	N/A	N/A	3000	medium
02	panTro4	24,129	3,309,577,922	2,902,338,967	407,238,955	% 51.29	Chimp	6X	143986469	SyntenicNet	93.112%	5000	medium
03	panPan1	10,867	2,869,190,071	2,725,905,606	143,284,465	% 36.53	Bonobo	26X	10124892	RecipBest	92.929%	3000	medium
04	gorGor3	46,823	3,029,553,646	2,822,760,080	206,793,566	% 48.80	Gorilla	2.1X	145327772	RecipBest	88.005%	3000	medium
05	ponAbe2	55	3,446,771,396	3,093,543,172	353,228,224	% 50.89	Orangutan	6X	135191526	SyntenicNet	89.187%	5000	medium
06	nomLeu3	17,492	2,962,077,449	2,756,609,047	205,468,402	% 51.14	Gibbon	5.6X	117381234	SyntenicNet	86.379%	3000	medium
07	nasLar1	319,550	3,011,982,740	2,397,109,760	614,872,980	% 46.33	Proboscis monkey	290X	137426304	RecipBest	74.541%	3000	medium
08	rhiRox1	319,549	3,011,966,170	2,397,093,190	614,872,980	% 46.33	Golden snub-nosed monkey	53.7X	137426304	RecipBest	74.547%	3000	medium
09	chlSab2	2,004	2,789,656,328	2,752,000,999	37,655,329	% 48.77	Green monkey	95X	101219884	SyntenicNet	84.393%	5000	medium
10	macFas5	7,601	2,946,843,737	2,803,866,385	142,977,352	% 50.11	Crab-eating macaque	68X	152835861	SyntenicNet	85.675%	3000	medium
11	rheMac3	34,103	2,969,988,180	2,639,145,830	330,842,350	% 48.54	Rhesus	50X	150158102	SyntenicNet	79.729%	5000	medium
12	papAnu2	63,250	2,948,380,710	2,893,250,291	55,130,419	% 38.95	Baboon	85X	139646187	SyntenicNet	84.179%	3000	medium
13	saiBol1	2,685	2,608,572,064	2,477,131,095	131,440,969	% 46.69	Squirrel monkey	80X	18744880	RecipBest	70.565%	3000	medium
14	calJac3	14,205	2,914,958,544	2,752,505,800	162,452,744	% 47.71	Marmoset	6X	132174527	SyntenicNet	71.709%	3000	medium
15	tarSyr2	337,189	3,453,864,774	3,405,755,564	48,109,210	% 47.85	Tarsier	48X	401181	RecipBest	56.022%	3000	medium
16	micMur1	185,042	2,902,270,736	1,852,394,361	1,049,876,375	% 37.31	Mouse lemur	2X	140884	RecipBest	42.653%	3000	medium
17	otoGar3	7,793	2,519,724,550	2,359,530,453	160,194,097	% 39.51	Bushbaby	137X	13852661	RecipBest	49.485%	3000	medium