Assemblathon 2 ‘bird’ Stats

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Here are the basic assembly stats for the bird data:  contig cutoff size=250bp

 


N:250 n:N50 N80 N50 N20 max sum name
Average 105054.3 8628.2 1235754.8 3899483.5 9540090.4 19342630.9 1.03E+09

849 57 2283 8580 20266 51162 1933317 bird_8C_contigs.fa

826 47 2930 11620 23347 57581 2026432 bird_8C_scaffolds.fa

70467 7137 15629 39414 87076 554547 1.04E+009 bird_6C_contigs.fa

16495 32 3207491 10011138 19098421 49826764 1.04E+009 bird_6C_scaffolds.fa

37670 4312 25386 67833 146481 671540 1.06E+009 bird_7C_contigs.fa

8062 23 2481996 10935449 37556899 50983430 1.06E+009 bird_7C_scaffolds.fa

190778 16265 6158 18177 38632 235482 1.07E+009 bird_10C_contigs.fa

92853 81 228034 2965671 8717439 32814605 1.07E+009 bird_10C_scaffolds.fa

54037 4855 18956 56996 141343 712654 1.10E+009 bird_11C_contigs.fa

4341 18 1833827 16806221 42927674 64643934 1.10E+009 bird_11C_scaffolds.fa

65217 5939 21833 53463 107654 666240 1.11E+009 bird_13E_contigs.fa

10697 23 6275406 14199076 31408994 65236555 1.11E+009 bird_13E_scaffolds.fa

66411 6094 20919 52129 105709 500974 1.11E+009 bird_14E_contigs.fa

10685 23 6278647 14202455 31417212 65264275 1.11E+009 bird_14E_scaffolds.fa

92575 7505 13282 39267 88316 666240 1.11E+009 bird_12C_contigs.fa

10703 23 6286291 14221761 31447220 65359764 1.11E+009 bird_12C_scaffolds.fa

75487 8235 16695 41221 80970 465622 1.17E+009 bird_4C_contigs.fa

34104 638 157708 516390 1104665 2942284 1.17E+009 bird_4C_scaffolds.fa

88197 2156 32923 134986 342996 1818605 1.17E+009 bird_3E_contigs.fa

41941 22 4805477 14768158 35825618 67706724 1.17E+009 bird_3E_scaffolds.fa

84487 1383 40265 193162 559349 2740960 1.17E+009 bird_2C_contigs.fa

41941 22 4815185 14777158 35841802 67755865 1.17E+009 bird_2C_scaffolds.fa

77515 3165 31975 102941 220703 849043 1.19E+009 bird_9C_contigs.fa

54666 177 405855 1746932 4194166 11487706 1.19E+009 bird_9C_scaffolds.fa

346930 5356 4039 50966 170544 1468602 1.31E+009 bird_1C_contigs.fa

293817 270 17136 894118 4140394 19295806 1.31E+009 bird_1C_scaffolds.fa

175676 21521 10126 23871 50265 424718 1.84E+009 bird_5C_contigs.fa

130759 7527 13236 38683 323074 4670483 1.84E+009 bird_5C_scaffolds.fa

486721 77970 1478 3334 7742 203381 9.98E+006 bird_15C_contigs.fa

486721 77970 1478 3334 7742 203381 9.98E+006 bird_15C_scaffolds.fa
  • dan

    Hi Matt, thanks for posting this. It looks like you have reported the scaffold stats in a way that ignores the captured gaps/runs of N’s within scaffolds. If its not too much of an imposition it would be useful to see the scaffold numbers (or even just the total scaffold lengths) including these gaps, which presumably represent sequences that are linked across but whose sequence is unknown (or found in erroneously unlinked short scaffolds).