Turkey: Difference between revisions
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| Line 29: | Line 29: | ||
nucmer -l 12 -c 65 -g 1000 -b 1000 | nucmer -l 12 -c 65 -g 1000 -b 1000 | ||
* | * Scf stats | ||
elem min q1 q2 q3 max mean n50 sum | elem min q1 q2 q3 max mean n50 sum | ||
aligned 24,336 66 1418 2176 5312 9558742 41836 1542391 | aligned 24,336 66 1418 2176 5312 9558742 41836 1542391 1,018,126,731 | ||
not_aligned 2,671 73 1120 1312 1640 24902 1597 1509 4,268,033 | |||
* Alignment stats (filter-q) | |||
. elem min q1 q2 q3 max mean n50 sum | |||
len 177171 12 1040 2379 5955 134409 4860 10218 861088419 | |||
%id 177171 11.24 80.94 84.76 87.69 100.00 83 85 14815276.23 | |||
Revision as of 23:05, 4 October 2009
Data
Chicken
- http://www.ncbi.nlm.nih.gov/genome/guide/chicken
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=10808
- http://dec2007.archive.ensembl.org/info/downloads/ftp_site.html
Stats:
elem min q1 q2 q3 max mean n50 sum Chr1..28,32,MT,W,Z 32 1028 5102438 13986235 37400442 200994015 32246882 94230402 1031900246 other 25 2911 35775 105415 246252 63870806 2743207 63870806 68580195 all 57 1028 105415 2031799 18911934 200994015 19306674 94230402 1100480441
Assembly2.0
Stats:
. elem min q1 q2 q3 max mean n50 sum ctg 145,663 64 1512 3433 8500 91891 6391 12594 930953352 scf 27,007 66 1354 1988 4793 9558742 37856 1538143 1022394764
Files:
/fs/szattic-asmg4/turkey/Assembly2.0/
Alignment to chicken
- Parameters:
nucmer -l 12 -c 65 -g 1000 -b 1000
- Scf stats
elem min q1 q2 q3 max mean n50 sum aligned 24,336 66 1418 2176 5312 9558742 41836 1542391 1,018,126,731 not_aligned 2,671 73 1120 1312 1640 24902 1597 1509 4,268,033
- Alignment stats (filter-q)
. elem min q1 q2 q3 max mean n50 sum len 177171 12 1040 2379 5955 134409 4860 10218 861088419 %id 177171 11.24 80.94 84.76 87.69 100.00 83 85 14815276.23