Turkey
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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 1,032,845,329 gaps(N's) 524913 1 30 64 254 1504285 268 792 141,055,297
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 1,233,186,341 all(gaps) 107061 25 100 100 100 500000 92 100 9,879,775 Chr1,1A,1B,2,3,4,4A,5..28,LG2,LG5,LGE22,M,Un,Z 37 9909 4907541 15652063 36305782 175225315 32343381 73657157 1,196,705,108
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 904,435,047 gaps 147792 100 100 100 100 2999 268 860 39,738,918
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 .
- Scaffolds with multiple alignment blocks
nl scfid chickenChr
1 7180002103050 2
2 7180002103154 6
3 7180002103203 3 25
4 7180002103204 10 28
5 7180002103206 18
6 7180002103213 4 26
7 7180002103242 5
8 7180002103280 1 8
9 7180002103298 7
10 7180002103329 6
11 7180002103402 8
12 7180002103421 9
13 7180002103425 2 7
14 7180002103431 6
15 7180002103433 1
16 7180002103480 5 6
17 7180002103500 12 13
18 7180002103519 3 9
19 7180002103555 6 18
20 7180002103557 8
21 7180002103561 3
22 7180002103574 1
23 7180002103597 2 17
24 7180002103605 2 3
25 7180002103608 8
26 7180002103614 2
27 7180002103617 2
28 7180002103618 1
29 7180002103619 11
30 7180002103620 4
31 7180002103621 1 2 28
32 7180002103627 1
33 7180002103637 6 7
34 7180002103638 2 18
35 7180002103642 4
36 7180002103648 1 3
37 7180002103653 1 5
38 7180002103663 6
39 7180002103668 1
40 7180002103669 8 9
41 7180002103670 1 4
42 7180002103672 2 3
43 7180002103675 1
44 7180002103677 1
45 7180002103679 2
46 7180002103681 1 5
47 7180002103682 1 21
48 7180002103683 4 17
49 7180002103684 13
50 7180002103685 1 2
51 7180002103686 1 3
52 7180002103688 3 8
53 7180002103693 12 15
54 7180002103694 1 2
55 7180002103695 3
56 7180002103698 2 12
57 7180002103702 6 11
58 7180002103714 4 5
59 7180002103715 1 2 4
60 7180002103717 2 10
61 7180002103720 1 6 7
62 7180002103723 4 6
63 7180002103725 1 14
64 7180002103728 1 9
65 7180002103736 1 5
66 7180002103740 7
67 7180002103742 1 3
68 7180002103743 6 8 17
69 7180002103744 1 17
70 7180002103750 2 3
71 7180002103752 9 18
72 7180002103762 2
73 7180002103771 1 3 19
74 7180002103798 7 26
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
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
Scf splits (Aleksey)
1 7180002103685 6 156 161 jumps from chr6 to chr1 4049114-4201400
2 7180002103648 1 45 79 1187881-1198679
3 7180002103620 241786-307810 # aligns to one chicken chr
4 7180002103280 56334-114382
5 7180002103762 386780-485750 # aligns to one chicken chr
6 7180002103638 111865-184832
7 7180002103743 707755-712324
8 7180002103743 1618441-1646472
9 7180002103743 1895159-1956617
10 7180002103683 3122611-3324351
11 7180002103642 536597-587034 # aligns to one chicken chr
12 7180002103204 94910-122663
13 7180002103681 5 33 57 jumps from chr5 to chr1 943178-1075454 map looks ok
14 7180002103715 9 243 270 jumps from chr3 to chr9 547913-610659 map looks ok
15 7180002103725 1 129 187 jumps from chr16 to chr1 1904425-2067581, map looks ok
16 7180002103728 11 83 131 jumps from chr11 to chr1 2456073-2532176, map looks ok
17 7180002103698 3 240 266 jumps from chr14 to chr3 588551-618407, map looks ok
18 7180002103686 1 34 41 jumps from chr2 to chr1 292876-340742, map look ok
19 7180002103621 3 40 57 jumps from chr1 to chr3 707868-766695, map looks ok
20 7180002103720 7 63 130 jumps from chr7 to chr13 1890283-1900965, map looks ok
21 7180002103682 23 68 75 jumps from chr1 to chr23 270646-281964, map looks ok
22 7180002103605 2 43 60 jumps from chr2 to chr3 1059724-1121629, map looks ok
23 7180002103688 10 131 162 jumps from chr10 to chr2 3129178-3331813, map looks ok
24 7180002103672 6 31 55 jumps from chr2 to chr6, 800904-850720, map looks ok
25 7180002103771 2 13 26 jumps from chr21 to chr2 516684-703439, map looks ok
26 7180002103519 11 52 62 jumps from chr11 to chr2 1685597-1695161, map looks ok
27 7180002103597 3 120 150 jumps from chr3 to chr19 2839516-3067987, map looks ok
28 7180002103717 3 61 96 jumps from chr3 to chr12, 2101452-2251116, map looks ok
29 7180002103743 10 101 257 jumps from chr8 to chr10, 3601251-3670472 map look ok,
30 7180002103743 jump from chr10 to chr19, 6212398-6251410 map looks ok
31 7180002103714 4 95 146 jumps from chr5 to chr4 1553913-1593600, map looks ok
32 7180002103723 4 133 179 jumps from chr9 to chr4 1656209-1721059, map looks ok
33 7180002103752 20 100 166 jumps from chr11 to chr20, 1951227-2017628,map looks ok
34 7180002103480 5 79 119 jumps from chr8 to chr5, 1086539-1133932, map looks ok
35 7180002103702 13 124 145 jumps from chr8 to chr13 935622-1070705, map looks ok
36 7180002103693 14 73 84 jumps from chr17 to chr14, 477273-532094, map looks ok
37 7180002103614 # aligns to one chicken chr
38 7180002103677 # aligns to one chicken chr
Annotation
Zebrafinch chr sample vs Chicken chr
- Sample 1Kbp every 1M in Zebrafinsh chr
ChickenChr ZebraChr count(>2) 1 chr1 406 1 chr1A 287 2 chr2 589 3 chr3 436 4 chr4 217 4 chr4A 77 5 chr5 244 6 chr6 132 7 chr7 155 8 chr8 116 9 chr9 103 10 chr10 108 11 chr11 105 12 chr12 88 13 chr13 75 14 chr14 65 15 chr15 56 17 chr17 49 18 chr18 45 19 chr19 53 20 chr20 63 21 chr21 26 22 chr22 11 23 chr23 20 24 chr24 32 26 chr26 14 27 chr27 13 28 chr28 14 Z chrZ 165 E22C19W28_E50C23 chrLGE22 3