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
A1 F2 I223 R1 9 19.6 1358936 97.3% 1322244 86.8

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGGTTACGCACCGTGGAAACGGATCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGTAAACTGGCGGCCTTTTATGATTCTCCAACCGGATTCCGTCATGGACCAAAATCGCTGGTCGATGACGAAACGCTGGTGGTGGTATTTGTCTCCA  >  NZ_CP009273/3275991‑3276184
                                                                                                   |                                                                                              
TGGTTACGCACCGTGGAAACGGATCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGT                                                                                                >  SRR3722107.638154/1‑100 (MQ=60)
 GGTTACGCACCGTGGAAACGGATCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGA                                                                                               >  SRR3722107.41758/1‑100 (MQ=60)
  GTTACGCACCGTGGAAACGGATCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAA                                                                                              >  SRR3722107.467550/1‑100 (MQ=60)
                       TCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAACTGGGGGCCCTTTTTGATTC                                                                         >  SRR3722107.23375/1‑100 (MQ=60)
                         GTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAAATGGCGGCCTTTTtttattttc                                                                       >  SRR3722107.295053/1‑91 (MQ=60)
                                           GGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAAATGGGGGCCTTTTTTGATTTTCCAACCGGGTTCCGTCATG                                                     >  SRR3722107.588044/1‑100 (MQ=60)
                                           GGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAAATGGCGGCCTTTTTTGATTTTCCAACCGGATTTCGTCATG                                                     >  SRR3722107.239111/1‑100 (MQ=60)
                                             CTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAACTGGCGGgcctttttgtttcccccacccgctccccccacggt                                                   >  SRR3722107.673365/1‑65 (MQ=60)
                                                ACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAACTGGCGGCCTTTTTTGATTTTCCCACCCGGTTCCGTCATGGGCCA                                                >  SRR3722107.245460/1‑100 (MQ=60)
                                                   GGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAACTGGCGGCCTTTTTTGATTCTCCAACCGGATTCCGTCATGGACCAAAA                                             >  SRR3722107.664961/1‑100 (MQ=60)
                                                          GCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGTAAAATGGCGGCCTTTTTTGATTTTCCAACCGGGTTCCGTCCTGGGCCAAAAACGCCGG                                      >  SRR3722107.666581/1‑100 (MQ=60)
                                                          GCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGGAAACCGGCGGCCTTTTTTAATTCTCCAACCGGATTTCGTCATGGCCCAAAATCttgct                                      >  SRR3722107.33062/1‑95 (MQ=60)
                                                                      GCGCTGAAAGTGCTGGAACTGACGGCGGGTAAACTGGCGGCCTTTTTTGATTCTCCcacccggttcccgcctgggccaaaaacgccgggcggtgacgaaa                          >  SRR3722107.622027/1‑56 (MQ=60)
                                                                                              GCGGGTAAAATGGCGGCCTTTTATGATTCTCCAACCGGATTCCGTCATGGACCAAAAACGCTGGTCGATGACGAAAAGCTGGGGGGGGGATTTGTCTCCA  >  SRR3722107.25543/1‑100 (MQ=60)
                                                                                                   |                                                                                              
TGGTTACGCACCGTGGAAACGGATCGTTTATCTCGGTAGCGGTGGCTTACAGGGCGCAGCACGCGAGTCGGCGCTGAAAGTGCTGGAACTGACGGCGGGTAAACTGGCGGCCTTTTATGATTCTCCAACCGGATTCCGTCATGGACCAAAATCGCTGGTCGATGACGAAACGCTGGTGGTGGTATTTGTCTCCA  >  NZ_CP009273/3275991‑3276184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑