Turkey
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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
- Ensembl download site
Chr 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
Zebrafinch (Taeniopygia guttata)
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=zebra%20finch
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19316 mitochondrion: NC_007897
- http://hgdownload.cse.ucsc.edu/downloads.html#zebrafinch
Chr stats:
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
Chr stats:
. elem min q1 q2 q3 max mean n50 sum Ch1..30,40,41 32 531 6400446 15119779 34928883 184590300 28263595 70426150 904435047
Assembly 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=151,843,863 (151M) 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/
Scaffold 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 1+alignments/scf 22045 1 1 1 2 1660 6 136 153866 2+alignments/2+chr 50 11625 55577 1398890 3387095 7409211 1883381 4298282 94,169,060
- Alignment stats
. elem min q1 q2 q3 max mean n50 sum len(all) 202105 11 681 1895 5189 134408 4315 10045 872,231,977 len(filter-1) 163390 12 1191 2673 6437 134409 5188 10410 847,715,057 %id(filter-1) 163390 11.24 81.10 84.82 87.68 100.00 83 85 .
Scaffold alignment to chicken
- Parameters:
nucmer -l 12 -c 65 -g 1000 -b 1000 delta-filter -1 # not yet
- Alignment stats
. elem min q1 q2 q3 max mean n50 sum len(all) 185138 11 600 2011 5567 134408 4407 10093 815928282 len(delta-filter -r) 155094 11 1065 2783 6592 134408 5165 10302 801185719 len(delta-filter -1) 148515 11 1144 2953 6836 134408 5341 10421 793361287
BACs.old
- Markers:
37918 : total CH260's 8558 : assembled in scaffolds
8641 : total 78TKNMI
- 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 1+markers/scf 1228 1 1 2 7 110 6 19 8,262 2+markers/2+chr 38 671404 1525677 2968427 4298282 7409211 3084380 4013969 117,206,475
BACs
- Scf len stats:
elem min q1 q2 q3 max mean n50 sum 1+markers 2478 1001 6013 36597 278486 9558742 365837 1830406 906,544,909 0 markers 24529 66 1323 1848 3839 325966 4722 11201 115,849,855 2+markers/2+chr 60 283784 1158965 2021582 3549120 7409211 2457241 3411361 147,434,495 3+markers/2+chr 38 426424 1609106 2833228 4013969 7409211 3061980 3819803 116,355,251
- Ctg len stats:
elem min q1 q2 q3 max mean n50 sum 1+markers 23077 76 6408 11837 19433 91891 14425 19768 332,889,618