Turkey: Difference between revisions
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| Line 50: | Line 50: | ||
* Scf stats | * Scf stats | ||
elem min q1 q2 q3 max mean n50 sum | elem min q1 q2 q3 max mean n50 sum | ||
1+alignments 22045 66 1450 2276 5670 9558742 45827 1562815 1,010,256,240 | |||
0alignments 4962 73 1159 1411 1935 119729 2446 2654 12,138,524 | |||
* Alignment stats (filter-1) | * Alignment stats (filter-1) | ||
| Line 72: | Line 71: | ||
scf7180002103752 18 5061302 10925261 1958581 4162033 7329248 5062809 440775 489825 214 -1 9.28 | scf7180002103752 18 5061302 10925261 1958581 4162033 7329248 5062809 440775 489825 214 -1 9.28 | ||
scf7180002103752 18 5061302 10925261 4163072 5060851 9929884 10866224 327663 376667 102 1 -5.76 | scf7180002103752 18 5061302 10925261 4163072 5060851 9929884 10866224 327663 376667 102 1 -5.76 | ||
= BACs = | |||
* Scf stats: | |||
elem min q1 q2 q3 max mean n50 sum | |||
1+markers 1228 1001 24541 247381 879303 9558742 696129 1984837 854,846,919 | |||
0markers 25779 66 1338 1911 4245 1214147 6499 26354 167,547,845 | |||
Revision as of 17:15, 7 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
Scf stats:
. elem min q1 q2 q3 max mean n50 sum <5K 20534 66 1257 1624 2346 5000 1976 2112 40582116 >5K 6475 5000 6876 13337 36546 9558742 151632 1605411 981822648
Reads:
TotalUsableReads=151843863 AvgClearRange=102 ContigReads=139021843(91.56%) DegenContigReads=8392124(5.53%) SurrogateReads=1317962(0.87%) SingletonReads=3314375(2.18%) Cvg=15X
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 1+alignments 22045 66 1450 2276 5670 9558742 45827 1562815 1,010,256,240 0alignments 4962 73 1159 1411 1935 119729 2446 2654 12,138,524
- Alignment stats (filter-1)
. elem min q1 q2 q3 max mean n50 sum len 163390 12 1191 2673 6437 134409 5188 10410 847,715,057 %id 163390 11.24 81.10 84.82 87.68 100.00 83 85 .
- Ambiguous alignments:
. elem min q1 q2 q3 max mean n50 sum multiple_locations 308 1058 3381 10254 46074 7409211 468379 3716226 144,260,908 multiple_chr 153 1213 4409 11625 61008 7409211 624239 4298282 95,508,695
Examples: scf7180002103561 3 5415215 113657789 1 1062596 10577164 11629376 229235 215157 84 1 -10.57 scf7180002103561 3 5415215 113657789 1063535 4213976 5596784 2394202 865958 916543 369 -1 6.66 scf7180002103561 3 5415215 113657789 4214015 5415182 3859 1218869 287310 294360 139 1 4.21 scf7180002103752 9 5061302 25554352 9555 1958541 20381314 18065068 612989 788008 264 -1 20.39 scf7180002103752 18 5061302 10925261 1958581 4162033 7329248 5062809 440775 489825 214 -1 9.28 scf7180002103752 18 5061302 10925261 4163072 5060851 9929884 10866224 327663 376667 102 1 -5.76
BACs
- Scf stats:
elem min q1 q2 q3 max mean n50 sum 1+markers 1228 1001 24541 247381 879303 9558742 696129 1984837 854,846,919 0markers 25779 66 1338 1911 4245 1214147 6499 26354 167,547,845