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)

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: 44 on different Chr; 30 on same chr
    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