[maq-help] Maq Output interpretation

[Girish B <bg...@he...>]

Hi there !

I am currently doing some illumina runs but I am having trouble to understand and interpret the outputs( Maq 0.6.8) ( Please check http://paste.pocoo.org/show/82004/). Of this, I am not sure I can understand the following :

1-  Why does maq do it in 3 rounds ?

2-   [match_core] processing sequence gi|157726890|ref|AC_000152.1|AC_000152 (59656706 bp)... Is this for chromosome 1? Because there seems to be 24 of them.

3- [mapping_count_single] 7, 11, 16, 33. What does that mean ?

4- match_data2mapping] 5 pairs are added afterwards.
    [match_data2mapping] (2279, 2338) reads are moved to meet paired-end requirement.
    [match_data2mapping] quality counts of the first reads: (2, 2277); second reads (5, 2333)
    [cal_insert_size] 5255 read pairs counted. insert size: 139.748240 +/- 10.506596

5-  [align_candidate] gi|157726890|ref|AC_000152.1|AC_000152: (1, 2, 6) out of 16
    [align_candidate] gi|157728228|ref|AC_000153.1|AC_000153: (0, 1, 5) out of 6
    [align_candidate] gi|157729478|ref|AC_000154.1|AC_000154: (0, 0, 13) out of 19

6-  and finally [match_data2mapping] 39592 out of 40180 raw reads are mapped with 38222 in pairs.
--   (total, isPE, mapped, paired) = (40180, 1, 39592, 38222)


Many thanks, 

Girish B