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=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/

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 (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         .

BACs

• 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