HI All,
I would be greatful if you could share me your knowledge in parsing the blastn file. I have a blastn output file, which is something like this 
ALIGNMENTS
>lcl|14079 ref|NC_000009.11|:4900000-5300000 Homo sapiens chromosome 9
+, 
GRCh37 primary reference assembly
Length=400001
 Score =  270 bits (146),  Expect = 2e-74
 Identities = 148/149 (99%), Gaps = 0/149 (0%)
 Strand=Plus/Minus

Query  1      TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  60
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48784  TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  48725

Query  61     AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  120
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48724  AATGGGATCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  48665

Query  121    ACAGGCAACCTACAGAATGGGAGAACATT  149
              |||||||||||||||||||||||||||||
Sbjct  48664  ACAGGCAACCTACAGAATGGGAGAACATT  48636

[download]

I would like to create a summary of the position of mismatch, and the type (insertion/deletion) from the blast output. In this case, the position 75, and the alleles A-C.

I tried with BioSearchIO, which parses the percentage, start and the end position of the alignment.Obviously, I dont want to have them in my summary rather the corodinates of mismatch, type of variation. Have any one know about any modules in perl/or a simpler(even harder) way of finding the position of mismatch and the type of variation?

In reply to parsing mismatch from blast output by Anonymous Monk

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