Turkey: Difference between revisions
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| Line 34: | Line 34: | ||
* Scf stats | * Scf stats | ||
elem min q1 q2 q3 max mean n50 sum | elem min q1 q2 q3 max mean n50 sum | ||
aligned 22045 66 1450 2276 5670 9558742 45827 1562815 1010256240 | |||
not_aligned 4962 73 1159 1411 1935 119729 2446 2654 12138524 | |||
* Alignment stats (filter-1) | * Alignment stats (filter-1) | ||
. elem min q1 q2 q3 max mean n50 sum | |||
. elem | len 163390 12 1191 2673 6437 134409 5188 10410 847715057 | ||
%id 163390 11.24 81.10 84.82 87.68 100.00 83 85 . | |||
Revision as of 14:14, 5 October 2009
Data
Chicken (Gallus gallus)
- 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,E22C19W28_E50C23,E64 34 1028 4512026 12968165 30671729 200994015 30377803 94230402 1032845329
Turkey (Meleagris gallopavo)
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Meleagris
- http://www.biolbull.org/cgi/content/abstract/61/2/157
- http://www.ncbi.nlm.nih.gov/sites/gquery?term=Meleagris+gallopavo[organism]
Assembly2.0
Stats:
. elem min q1 q2 q3 max mean n50 sum scf 27,007 66 1354 1988 4793 9558742 37856 1538143 1022394764 ctg 145,663 64 1512 3433 8500 91891 6391 12594 930953352 deg 440,796 64 102 256 485 8055 312 483 137835235
Files:
/fs/szattic-asmg4/turkey/Assembly2.0/
Alignment to chicken
- Parameters:
nucmer -l 12 -c 65 -g 1000 -b 1000 delta-filter -1
- Scf stats
elem min q1 q2 q3 max mean n50 sum
aligned 22045 66 1450 2276 5670 9558742 45827 1562815 1010256240
not_aligned 4962 73 1159 1411 1935 119729 2446 2654 12138524
- Alignment stats (filter-1)
. elem min q1 q2 q3 max mean n50 sum len 163390 12 1191 2673 6437 134409 5188 10410 847715057 %id 163390 11.24 81.10 84.82 87.68 100.00 83 85 .