BWA Alignment problems ..
It also produced a wrong CIGAR string.
NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.....GGCTCAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG.......... Query (Correct Alignment)
BWA 0.5.0 (Version)
Cigar String: 3S1M4D72M
NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.........T----CAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG..... BWA alignment
The 0.5.5 version showed no alignments for the same query and target sequences.
It also produced a wrong CIGAR string.
NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.....GGCTCAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG.......... Query (Correct Alignment)
BWA 0.5.0 (Version)
Cigar String: 3S1M4D72M
NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.........T----CAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG..... BWA alignment
The 0.5.5 version showed no alignments for the same query and target sequences.