Turkey

Data

Chicken (Gallus gallus)

• http://www.ncbi.nlm.nih.gov/genome/guide/chicken
• http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=10808
• http://dec2007.archive.ensembl.org/info/downloads/ftp_site.html

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

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]

Assembly2.0

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=151843863
 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/

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              22045       66     1450   2276   5670   9558742    45827      1562815    1,010,256,240  
 not_aligned          4962        73     1159   1411   1935   119729     2446       2654       12,138,524
     

• Alignment stats (filter-1)

 .                    elem        min    q1     q2     q3     max        mean       n50        sum
 len                  163390      12     1191   2673   6437   134409     5188       10410      847,715,057
 %id                  163390      11.24  81.10  84.82  87.68  100.00     83         85         .

• Ambiguous alignments:

 .                    elem       min    q1     q2     q3     max        mean       n50        sum
 multiple_locations   308        1058   3381   10254  46074  7409211    468379     3716226    144,260,908
 multiple_chr         153        1213   4409   11625  61008  7409211    624239     4298282    95,508,695

 Examples:
 scf7180002103561 3 5415215 113657789   1       1062596   10577164 11629376   229235 215157 84 1 -10.57
 scf7180002103561 3 5415215 113657789   1063535 4213976   5596784  2394202    865958 916543 369 -1 6.66
 scf7180002103561 3 5415215 113657789   4214015 5415182   3859     1218869    287310 294360 139 1 4.21

 scf7180002103752 9  5061302 25554352   9555    1958541   20381314 18065068   612989 788008 264 -1 20.39
 scf7180002103752 18 5061302 10925261   1958581 4162033   7329248  5062809    440775 489825 214 -1 9.28
 scf7180002103752 18 5061302 10925261   4163072 5060851   9929884  10866224   327663 376667 102 1 -5.76