Turkey

Data

Chicken

• 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   32         1028   5102438 13986235 37400442 200994015  32246882   94230402   1031900246     
other                25         2911   35775   105415   246252   63870806   2743207    63870806   68580195       
all                  57         1028   105415  2031799  18911934 200994015  19306674   94230402   1100480441

Assembly2.0

Stats:

 .                    elem        min    q1     q2     q3     max        mean       n50        sum
 ctg                  145,663     64     1512   3433   8500   91891      6391       12594      930953352
 scf                  27,007      66     1354   1988   4793   9558742    37856      1538143    1022394764

Files:

 /fs/szattic-asmg4/turkey/Assembly2.0/

Alignment to chicken

• Parameters:

 nucmer -l 12 -c 65 -g 1000 -b 1000

• Scf stats

                      elem        min    q1     q2     q3     max        mean       n50        sum            
 aligned              24,336      66     1418   2176   5312   9558742    41836      1542391    1,018,126,731  
 not_aligned          2,671       73     1120   1312   1640   24902      1597       1509       4,268,033

• Alignment stats (filter-q)

                     elem         min    q1     q2     q3     max         mean       n50        sum            
 len                 177171       12     1040   2379   5955   134409      4860       10218      861088419      
 %id                 177171       11.24  80.94  84.76  87.69  100.00      83         85         .