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

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    1010256240  
 not_aligned          4962        73     1159   1411   1935   119729     2446       2654       12138524
     

• Alignment stats (filter-1)

 .                    elem        min    q1     q2     q3     max        mean       n50        sum
 len                  163390      12     1191   2673   6437   134409     5188       10410      847715057
 %id                  163390      11.24  81.10  84.82  87.68  100.00     83         85         .