Turkey: Difference between revisions
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len(filter-1) 163390 12 1191 2673 6437 134409 5188 10410 847,715,057 | 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 . | %id(filter-1) 163390 11.24 81.10 84.82 87.68 100.00 83 85 . | ||
len(subset 10)* 2952 12 771 2202 5413 45094 4040 8052 11926507 | |||
id%(subset 10) 2952 33.22 80.56 84.51 87.68 100.00 83 84 . | |||
= Scaffold alignment to zebrafinch = | |||
* Parameters: | |||
nucmer -l 12 -c 65 -g 1000 -b 1000 | |||
delta-filter -1 | |||
* Alignment stats (44 scf : subset 10) | |||
. elem min q1 q2 q3 max mean n50 sum | |||
len(subset 10)* 5286 12 233 485 860 12853 675 1033 3570025 | |||
%id(subset 10) 5286 40.99 74.20 78.57 85.63 100.00 80 79 . | |||
= Chromosome alignment to chicken = | = Chromosome alignment to chicken = | ||
Revision as of 16:05, 30 October 2009
Data
Chicken (Gallus gallus)
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 gaps(N's) 524913 1 30 64 254 1504285 268 792 141055297
Files:
/fs/szasmg3/dpuiu/chicken/
Zebrafinch (Taeniopygia guttata)
Chr stats:
. elem min q1 q2 q3 max mean n50 sum all(random dumplication) 70 9909 369730 2517995 16419078 175225315 17616947 73657157 1233186341 all(gaps) 107061 25 100 100 100 500000 92 100 9879775 Chr1,1A,1B,2,3,4,4A,5..28,LG2,LG5,LGE22,M,Un,Z 37 9909 4907541 15652063 36305782 175225315 32343381 73657157 1196705108
Files:
/fs/szasmg3/dpuiu/zebrafinch/
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]
Files:
/fs/szasmg3/dpuiu/turkey/
Assembly2.0
Stats:
. elem min q1 q2 q3 max mean n50 sum Ch1..30,40,41 32 531 6400446 15119779 34928883 184590300 28263595 70426150 904435047 gaps 147792 100 100 100 100 2999 268 860 39738918
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 . len(subset 10)* 2952 12 771 2202 5413 45094 4040 8052 11926507 id%(subset 10) 2952 33.22 80.56 84.51 87.68 100.00 83 84 .
Scaffold alignment to zebrafinch
- Parameters:
nucmer -l 12 -c 65 -g 1000 -b 1000 delta-filter -1
- Alignment stats (44 scf : subset 10)
. elem min q1 q2 q3 max mean n50 sum len(subset 10)* 5286 12 233 485 860 12853 675 1033 3570025 %id(subset 10) 5286 40.99 74.20 78.57 85.63 100.00 80 79 .
Chromosome 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
- Mapping (200+ alignments)
chickenChr turkeyChr #alignments 1 Chr1 35025 2 Chr3 18143 2 Chr6 7612 3 Chr2 17765 4 Chr4 11226 4 Chr9 2132 5 Chr5 8516 6 Chr8 4552 7 Chr7 4394 8 Chr10 3654 9 Chr11 2729 10 Chr12 2500 11 Chr13 2629 12 Chr14 2158 13 Chr15 2136 14 Chr16 2109 15 Chr17 1524 17 Chr19 1285 18 Chr20 1374 19 Chr21 1155 20 Chr22 1828 21 Chr23 887 22 Chr24 511 23 Chr25 751 24 Chr26 862 26 Chr28 592 27 Chr29 568 28 Chr30 553 Z Chr41 4178 Z Chr1 404
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