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 I202 R1 3 42.2 2248258 97.5% 2192051 86.8

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGTAACGGGCGTCAGGCCGGTGGCGGTCAGCAATTGTGTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAATACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTCGTCGTGGTTTGATATTCAGGCACCACACGAC  >  NZ_CP009273/2162787‑2162981
                                                                                                 |                                                                                                 
GGTAACGGGCGTCAGGCCGGTGGCGGTCAGCAATTGTGTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAAGAC                                                                                                 >  SRR3722084.829237/1‑100 (MQ=60)
GGTAACGGGCCTCAGGCCGGTGGCCGTCAGCAATTGTGTCCGAACGCCTTAATTAACGATGGTTTGCTGCCACTGCGCATTTTTACCGGCGATGAAAGAC                                                                                                 <  SRR3722084.1057308/100‑1 (MQ=60)
       GGCGTCAGGCCGGTGGCGGTCAGCAATTGTGTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAATACTTCCGGC                                                                                          <  SRR3722084.587285/100‑1 (MQ=60)
                  GGTGGCGGTCAGCAATTGTGTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAAGACTTCCGGCTCTCGTATCAA                                                                               >  SRR3722084.717794/1‑100 (MQ=60)
                                     GTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAATACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGA                                                            >  SRR3722084.96231/1‑100 (MQ=60)
                                                 TAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAAGACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATAT                                                <  SRR3722084.879758/100‑1 (MQ=60)
                                                                TGCTGCAACTGCGCATTTTTACCGGCGATGAAAGACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTC                                 >  SRR3722084.882531/1‑100 (MQ=60)
                                                                       ACTGCGCATTTTTACCGGCGATGAAAGACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTCGTCGTGG                          <  SRR3722084.732700/100‑1 (MQ=60)
                                                                                              AAATACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTCGTCGTGGTTTGATATTCAGGCACCACACGA   >  SRR3722084.313610/1‑100 (MQ=60)
                                                                                               AAGACTTCCCGCTCTCATATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTCGTCGTGGTTTGATATTCAGGCACCACACGAC  <  SRR3722084.1032091/100‑1 (MQ=60)
                                                                                                 |                                                                                                 
GGTAACGGGCGTCAGGCCGGTGGCGGTCAGCAATTGTGTCCGAACGCGTTAATTAACGATGGCTTGCTGCAACTGCGCATTTTTACCGGCGATGAAATACTTCCGGCTCTCGTATCAACCTTAAAATCTGACGAAGATAACCCGAATATTATCGAAGGCGCTTCGTCGTGGTTTGATATTCAGGCACCACACGAC  >  NZ_CP009273/2162787‑2162981

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑