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  • zcrself
    Junior Member
    • Sep 2009
    • 5

    #1

    the format of output file of Maq

    Code:
    HWI-EAS-249_42:1:1:10:282#0/2	chromosome01	8649295	-	0	0	0	0	0	11	20	0	12	76	aattccaaggagcctgcttgacctgtgtttcgtctgaacttcaaccctcctcgatgctgcttctctaagctgaacT	########################################!############################;4864:A
    HWI-EAS-249_42:1:1:10:1227#0/2	chromosome01	8757671	-	0	0	19	19	19	10	25	0	0	76	gagtcgttaaaaaaaatctatttcttagggttatttcttgggggacggaagattatactccccccgtcctataatA	#########################################9;9(;779479(949(9;98;;8;78679696;9B
    HWI-EAS-249_42:1:1:12:1701#0/2	chromosome01	11998357	+	0	0	19	19	19	15	36	0	0	76	CaacGGattggctggtgacaccgatatctgactttatggctcgcgcctgtggtgggacccagcgtcgtgggcgggg	B55,??335###################################################################
    HWI-EAS-249_42:1:1:11:1076#0/2	chromosome01	12313108	-	0	0	6	6	6	6	10	0	0	76	aaatcagcttcccaagatgtcgtacccccagaatggtcataatttacggatgttctcatttcattaacaaaaCCtT	##########################################!#############################@?0?
    HWI-EAS-249_42:1:1:11:637#0/2	chromosome01	13502430	+	0	0	19	19	19	6	12	0	0	76	cggatttaattggatagatatatctatacggttaaacttgagtgcaggacctccgactggttcacctatacgcact	############################################################################
    this file was produced by Maq-0.7.1
    what means of every columns?
  • zcrself
    Junior Member
    • Sep 2009
    • 5

    #2
    the format of map which is produced by Maq

    read name, chromosome, position, strand, insert size from the outer coorniates of a pair, paired flag, mapping quality, single-end mapping quality, alternative mapping quality, number of mismatches of the best hit, sum of qualities of mismatched bases of the best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp on the reference, length of the read, read sequence and its quality

    Comment

    • nilshomer
      Nils Homer
      • Nov 2008
      • 1283

      #3
      Originally posted by zcrself View Post
      read name, chromosome, position, strand, insert size from the outer coorniates of a pair, paired flag, mapping quality, single-end mapping quality, alternative mapping quality, number of mismatches of the best hit, sum of qualities of mismatched bases of the best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp on the reference, length of the read, read sequence and its quality
      See:
      http://maq.sourceforge.net/maq-manpage.shtml
      http://maq.sourceforge.net/maqmap_format.shtml

      Comment

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