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 chicken.len
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 zebrafinch.len
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: preliminary
. 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
Stats: final
elem min q1 q2 q3 max mean n50 sum Ch1..30,40,41 32 531 7024757 18811362 37793329 207174646 31576111 75696247 1,010,435,575 Ch1..30,40,41,Un 33 531 7024757 18811362 37793329 207174646 32954439 75696247 1,087,496,503 turkey.len
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
Assembly stats(all):
. elem min q1 q2 q3 max mean n50 sum scf 27,007 66 1354 1988 4793 9558742 37856 1538143 1,022,394,764 ctg 145,663 64 1512 3433 8500 91891 6391 12594 930,953,352 deg 440,796 64 102 256 485 8055 312 483 137,835,235
Assembly stats(placed): preliminary AGP
. elem min q1 q2 q3 max mean n50 sum scf 2,504 1001 5868 35589 272564 9558742 362085 1830406 906,662,877 ctg 111,752 64 1919 4886 10524 91891 7616 13635 851,209,123 deg 36,072 64 144 331 530 8055 373 521 13,487,006 ctg+deg 147,824 64 520 2783 8197 91891 5849 13426 864,696,129
Assembly stats(placed by synteny): final AGP
. elem min q1 q2 q3 max mean n50 sum ctg 131,217 64 1651 3975 9289 91891 6866 12989 901,044,472 deg 31,426 64 128 283 530 8055 357 540 11,241,382 ctg+deg 162,643 64 731 2602 7576 91891 5609 12829 912,285,854
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 aligned 22,045 66 1450 2276 5670 9558742 45827 1562815 1,010,256,240 unaligned 4,962 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
- Ctg stats (ctgs in aligned scaff)
elem min q1 q2 q3 max mean n50 sum aligned 139790 64 1580 3665 8822 91891 6585 12739 920,634,899 unaligned 5873 64 1148 1399 1887 22071 1756 1766 10,318,453
- 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 .
- turkey scf vs chicken & turkey chr : 15% of the scaffold sequence seem to align in opposite orientation !!! Could the scaffold be misoriented by mistake?
. elem min q1 q2 q3 max mean n50 sum opposite 1527 925 2604 7579 32323 6964320 78342 1018939 119629225 same 2619 97 2591 11510 128530 9558742 306323 1873938 802261737
Mapping
- (200+ alignments)
chickenChr turkeyChr #alignments 1 Chr1 35025 2 Chr3 18143 : Chr6 followed by Chr3 2 Chr6 7612 3 Chr2 17765 : Chr2 5' flipped 4 Chr4 11226 : Chr6 followed by Chr4 4 Chr9 2132 5 Chr5 8516 6 Chr8 4552 7 Chr7 4394 8 Chr10 3654 : Chr10 5' flipped 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 : Chr20 3' flipped 19 Chr21 1155 20 Chr22 1828 21 Chr23 887 22 Chr24 511 23 Chr25 751 24 Chr26 862 25 Chr27 3 26 Chr28 592 27 Chr29 568 28 Chr30 553 Z Chr41 4178 Z Chr1 404 W Chr41 24 E22C19W28_E50C23 ChrUn 7l E64 ChrUn 20
- Scaffolds with multiple alignment blocks:
- 44 on different Chr
- 30 on same chr; 11 appear to be partially flipped
nl scfid chickenChr
1 7180002103050 2
2 7180002103154 6
3 7180002103203 3 25 # new
4 7180002103204 10 28
5 7180002103206 18
6 7180002103213 4 26 # new
7 7180002103242 5 # partially flipped
8 7180002103280 1 8
9 7180002103298 7
10 7180002103329 6 # partially flipped
11 7180002103402 8 # partially flipped
12 7180002103421 9
13 7180002103425 2 7 # new
14 7180002103431 6 # partially flipped
15 7180002103433 1 # partially flipped
16 7180002103480 5 6
17 7180002103500 12 13 # new
18 7180002103519 3 9
19 7180002103555 6 18 # new
20 7180002103557 8
21 7180002103561 3
22 7180002103574 1
23 7180002103597 2 17 # new
24 7180002103605 2 3 # new
25 7180002103608 8
26 7180002103614 2
27 7180002103617 2 # partially flipped
28 7180002103618 1 # partially flipped
29 7180002103619 11 # partially flipped
30 7180002103620 4
31 7180002103621 1 2 28
32 7180002103627 1
33 7180002103637 6 7 # new
34 7180002103638 2 18 # new
35 7180002103642 4
36 7180002103648 1 3
37 7180002103653 1 5 # new
38 7180002103663 6
39 7180002103668 1
40 7180002103669 8 9 # new
41 7180002103670 1 4 # new
42 7180002103672 2 3
43 7180002103675 1 # partially flipped
44 7180002103677 1
45 7180002103679 2 # partially flipped
46 7180002103681 1 5
47 7180002103682 1 21
48 7180002103683 4 17
49 7180002103684 13 # partially flipped
50 7180002103685 1 2
51 7180002103686 1 3
52 7180002103688 3 8
53 7180002103693 12 15
54 7180002103694 1 2 # new
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 # new
62 7180002103723 4 6
63 7180002103725 1 14
64 7180002103728 1 9 # new
65 7180002103736 1 5 # new
66 7180002103740 7
67 7180002103742 1 3 # new
68 7180002103743 6 8 17
69 7180002103744 1 17 # new
70 7180002103750 2 3 # new
71 7180002103752 9 18
72 7180002103762 2
73 7180002103771 1 3 19
74 7180002103798 7 26 # new
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
Split ids: cat Chr_preliminary.agp | grep W | grep -v ChrUn | awk '{print $11}' | grep ^7181 | sort -u | nl
1 7181002103204
2 7181002103280
3 7181002103480
4 7181002103519
5 7181002103620
6 7181002103621
7 7181002103648
8 7181002103672
9 7181002103681
10 7181002103682
11 7181002103683
12 7181002103685
13 7181002103686
14 7181002103688
15 7181002103693
16 7181002103698
17 7181002103702
18 7181002103714
19 7181002103715
20 7181002103717
21 7181002103723
22 7181002103725
23 7181002103743
24 7181002103752
25 7181002103771
Zebrafinch chr sample vs Chicken chr
- Sample 1Kbp every 1M in Zebrafinsh chr
ChickenChr ZebraChr count(>2) 1 chr1 406 1* chr1A 287 1* chr1B 124 # not sampled 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 16 nothing 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 W chrZ 30 # not sampled E64 nothing E22C19W28_E50C23* chrLGE22 3
Synteny
MSU:
"We do see a couple of very small translocations between chromosomes 1 and 4,but these are so small that they could be errors in the chicken assembly or, more likely, paralogous sequences that perhaps were two copies in the last common ancestor and chicken kept one and turkey the other. We don't see translocations between chromosomes Z and 1, so I expect that these alignments are due to a repetitive element (CR1 being the most likely), but the Z assembly is tentative even in chicken, so it's hard to be sure."
Syntenic regions:
chickenRegions turkeyRegions chickenChr turkeyChr all 209166 311363 # nucmer -l 12 -c 65 -g 1000 -b 1000 filter-1 183058 259760 142 186 # delta-filter -1 filter 170658 239592 125 129 # filter-anc.pl -maxDist 200000 -W 20 -p 0.1 merge0 3260 2250 125 130 # merge-anc.pl -maxDist 200000 merge1 1573 1368 110 93 # merge-anc.pl -maxDist 200000 -minCount 8 -minLen 10000 merge2 376 488 49 47 # merge-anc.pl -maxDist 1000000 -minCount 20 -minLen 100000
Problems
ctg7180001625741
- 1 ctg scaff: 7180002083787(1.4Kbp)
- Single links to 2 diff scaff: 7180002103637 & 7180002103666
- Synteny info (Daniela)
cat /fs/szasmg3/dpuiu/turkey/Alignment2.0/chicken-turkey.ctg/turkey.ctg.posmap.merge | grep -C 20 7180001625741 # chickenChr turkeyChr 7180002057801 6 36246991 36257816 -1 Chr8 35888371 35899195 r U 100 7180001625741 6 36269529 36271001 -1 . . . . . . ... 7180002074579 6 36382217 36386350 -1 Chr8 35899296 35903428 r N 20910
- Synteny info (Aleksey)
cat /fs/ftp-cbcb/pub/data/turkey/Assembly2.0/place_by_sinteny/contigs.chicken.order.with_AGP.valid.txt | grep -C 1 7180001625741 | pretty # chickenChr turkeyChr 1 1790 36269140 36267359 7180001578245 chr6 Chr7 20109532 20111855 2324 - 7180001578245 307 1472 36270694 36269529 7180001625741 chr6 ChrUn 32131240 32132711 1472 0 7180001625741* 2343 5341 36282706 36279707 7180001914610 chr6 Chr7 36045401 36052860 7460 - 7180001914610
cat turkey.posmap.ctgscf | grep 7180002103637 | egrep -n '7180001578245|7180001914610' ... 302:7180001914610 7180002103637 2403512 2410972 f 391:7180001578245 7180002103637 3013067 3015391 f ... 463:
Scf 7180002103637 aligns both to Chr6 & Chr7
cat /fs/szasmg3/dpuiu/turkey/Alignment2.0/chicken-turkey.scf/turkey.scf-chicken.filter-1.merge0.anc | grep 7180002103637 7180002103637 7 3817505 38384769 2 2285066 23413757 21084724 651501 705639 284 -1 23.41 7180002103637 6 3817505 37400442 2285109 2410972 36410067 36277407 37596 43600 21 -1 38.69 7180002103637 7 3817505 38384769 2410993 3817505 21084676 19700317 384609 354790 151 -1 23.49
grep 7180002103637 /fs/szasmg3/dpuiu/turkey/BACs/BAC_map_final.txt | pretty | sort -nk9 | nl
1 CH260098J15_SP6 7_10 7 21623779 150000 7180001914412 7180002103637 2833 2833
2 78TKNMI023L02_SP6 7_10 7 21655259 150000 7180001914413 7180002103637 462 8036
3 78TKNMI020I14_T7 7_10 7 21786579 150000 7180001914413 7180002103637 6568 14142
...
91 78TKNMI028M05_T7 8_13 8 34451891 150000 7180001914600 7180002103637 4694 2314126
92 CH260110M21_T7 8_13 8 34375922 150000 7180001914602 7180002103637 4382 2344157
93 CH260102C12_T7 8_13 8 34561953 150000 7180001914608 7180002103637 7429 2400413
...
155 CH260102B06_SP6 7_10 7 18173403 150000 7180001914714 7180002103637 578 3753466
156 CH260091G02_T7 7_10 7 18147518 150000 7180001914716 7180002103637 14232 3777334
157 78TKNMI020K20_T7 7_10 7 17944915 150000 7180001914719 7180002103637 5969 3809779