Table 3

Cross-species comparisons of contig transcripts.


# contigs

 # missing
in ASa
 # missing
in RTb
 # missing
in bothc
 % sim
to ASd
 Avelene

 % sim
to RTf
 Avelen
Atlantic salmon (SJ)g
 5781
 479
 1210
 354
 98.4
 705
 93.4
 493
Atlantic salmon (all)h
 81398
 na
 36351
 na
 na
 na
 93.3
 504
Rainbow trout
 50256
 13626
 na
 na
 93.8
 495
 na
 na
Chinook salmon
 8517
 797
 1224
 426
 94.2
 510
 95.5
 510
Sockeye salmon
 6200
 577
 770
 298
 94.6
 571
 95.7
 569
Brook trout
 5424
 285
 627
 174
 94.4
 580
 93.9
 522
Lake whitefish
 6446
 804
 1420
 608
 92.5
 425
 92.2
 399
Grayling
 5408
 657
 1136
 506
 91.7
 435
 91.3
 400
Northern pike
 2380
 1894
 2001
 1846
 89.6
 241
 89.4
 251
Rainbow smelt
 12159
 7462
 7812
 6920
 86.2
 431
 86.1
 419

a number of contigs that are not found in the Atlantic salmon database

b number of contigs that are not found in the rainbow trout database

c number of contigs that are not found in either the Atlantic salmon or rainbow trout database

d percent identity compared to the top BLASTN hit to the Atlantic salmon database over 200 bp and e-value < 1e-25. In the case of Atlantic salmon (SJ) the comparison is to the McConnell strain.

e average length of the BLASTN hit

f percent identity compared to the top BLASTN hit to the rainbow trout database over 200 bp and e-value < 1e-25

g only Atlantic salmon ESTs from the Saint John River strain

h all Atlantic salmon ESTs other than those in note "g" above

Koop et al. BMC Genomics 2008 9:545   doi:10.1186/1471-2164-9-545