TupChi1 5-way Genome size statistics

see also

• Chinese tree shrew 5-way TupChi1 5-way conservation alignment
• Chinese tree shrew 5-way TupChi1 5-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 tupChi1 matched (chainLink table)	chain minScore	chain linearGap
01	tupChi1	50,750	2,846,580,235	2,706,389,135	140,191,100	% 40.02	Chinese tree shrew	80X	3670124	N/A	N/A	N/A	N/A
02	galVar1	179,514	3,187,660,572	2,802,837,430	384,823,142	% 38.66	Malayan flying lemur	55X	245189	RecipBest	52.252%	3000	medium
03	hg38	455	3,209,286,105	3,049,315,783	159,970,322	% 52.10	Human	20X	145138636	SyntenicNet	50.350%	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	41.225%	3000	medium
05	mm10	66	2,730,871,774	2,652,783,500	78,088,274	% 45.18	Mouse	20X	130694993	SyntenicNet	26.188%	3000	medium