Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F5 I177 R1 141 27.5 996908 97.7% 973979 124.3

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TAGCGGGATCGCCCGAGCAAATTTTGTTCTGCCATCCCATCGCGATGATCTGCTCAGGGGTATAAATATCAATGTTCTTACTGTCGATACACTGGTTAGTGTCGATGCGACTTTTTCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGCGTAGACATGCTCGCTTTCAAAGTTGCCGTTGGTATTGTT  >  NZ_CP009273/743988‑744231
                                                                                                                   |                                                                                                                                
gatgtattgtagtttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCTGGTTAGTGTCGATGCGACTTTTCCCCAGACTGGCATCGTAATCGACACCGTTGTATGT                                                                                               <  SRR3722131.80409/60‑1 (MQ=60)
                                 ATCCCATCGCGATGATCTGCTCAGGGGTATAAATATCAATGTTCTTACTGTCGATACACTGGTTAGTGTCGATGCGACTTTTTCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCC                                                              >  SRR3722131.161964/1‑151 (MQ=60)
                                      ATCGCGATGATCTGCTCAGGGGTATAAATATCAATGTTCTTACTGTCGATACACTGGTTAGTGTCGATGCGACTTTTCCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGAT                                                         <  SRR3722131.40068/151‑1 (MQ=60)
                                           GATGATCTGCTCAGGGGTATAAATATCAATGTTCTTACTGTCGATACACTGGTTAGTGTCGATGCGACTTTTCCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGG                                                    <  SRR3722131.287547/151‑1 (MQ=60)
                                                                                  GTCGATACACTGGTTAGTGTCGATGCGACTTTTTCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGCGTAGACATGCTCGCTTTCAAAGTTGCCG             >  SRR3722131.53049/1‑151 (MQ=60)
                                                                                          ACTGGTTAGTGTCGATGCGACTTTTTCCCAGACTGGAATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGAGTAGACATGCTCGCTTTCAAAGTTGCCGTTGGTATT     >  SRR3722131.231397/1‑151 (MQ=60)
                                                                                             GGTTAGTGTCGATGCGACTTTTCCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGCGTAGACATGCTCGCTTTCAAAGTTGCCGTTGGTATTGTT  >  SRR3722131.377938/1‑151 (MQ=60)
                                                                                             GGTTAGTGTCGATGCGACTTTTCCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGCGTAGACATGCTCGCTTTCAAAGTTGCCGTTGGTATTGTT  >  SRR3722131.401865/1‑151 (MQ=60)
                                                                                                                   |                                                                                                                                
TAGCGGGATCGCCCGAGCAAATTTTGTTCTGCCATCCCATCGCGATGATCTGCTCAGGGGTATAAATATCAATGTTCTTACTGTCGATACACTGGTTAGTGTCGATGCGACTTTTTCCCAGACTGGCATCGTAATCGACACCGTTGTATGTCACGCCGAGTTGATAATAACGATCCTGCACCCCCGGATAGGGGTTTACCCAGGCGTAGACATGCTCGCTTTCAAAGTTGCCGTTGGTATTGTT  >  NZ_CP009273/743988‑744231

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑