Turkey: Difference between revisions

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Line 91: Line 91:
   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)

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

Annotation