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
TTCACATCCTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGTGGGTCTTTGCCAGCATCTTCAGCAATATCAACCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCACGGGCAGTGAC  >  NZ_CP009273/4501738‑4501920
                                                                                                |                                                                                      
TTCACATCCTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGTGGG                                                                                     <  SRR3722084.608485/100‑1 (MQ=60)
        CTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGGCTTTGCC                                                                             >  SRR3722084.25181/1‑100 (MQ=60)
        CTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGGCTTTGCC                                                                             >  SRR3722084.318147/1‑100 (MQ=60)
        CTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGGCTTTGCC                                                                             >  SRR3722084.64833/1‑100 (MQ=60)
                         TCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGTGGGTCTTTGCCAGCATCTTCAGCAATAT                                                            <  SRR3722084.268274/100‑1 (MQ=60)
                            GATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGGCTTTGCCAGCATCTTCAGCAATATCAA                                                         >  SRR3722084.646996/1‑100 (MQ=60)
                               ACTCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGTGGGTCTTTGCCAGCATCTTCAGCAATATCAACCC                                                      <  SRR3722084.638528/100‑1 (MQ=60)
                                            GGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGTCTTTGCCAGCCTCTTCAGCAATATCAACCCCGCCATGCCGCCC                                         >  SRR3722084.507953/1‑100 (MQ=60)
                                             GCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGGGGGGCTTTGCCAGCATCTTCAGCAATATCAACCCCGCCCTGCCGCCCG                                        >  SRR3722084.828697/1‑100 (MQ=60)
                                                                     CCGGTGAGCGCCAGCTTCATCGGCTGGGGGGTCTTTGCCAGCATCTTCAGCAATATCAACCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCA                >  SRR3722084.951767/1‑100 (MQ=60)
                                                                        GTGAGCGCCAGCTTCCTCGGCTGGTGGGTTTTTGCCAGCATCTTCAGCAATATCACCCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCA             <  SRR3722084.78364/100‑1 (MQ=60)
                                                                        GTGAGCCCCAGTTTCACCGGCTGGGGGGTCTTTGCCAGCATCTTCAGAAATATCACCCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCA             <  SRR3722084.241084/100‑1 (MQ=60)
                                                                           GGCGCCAGCTTCACCGGCGGGGGGGTTTTTGCCAGCATCTTCAGAAATATCACCCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCACGG          <  SRR3722084.188194/100‑1 (MQ=60)
                                                                                   CTCCAGCGGCTGGTGGGTCTTTGCCACCTTCTTCAGCAATATCACCCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCACGGGCAGTGAC  <  SRR3722084.147652/100‑1 (MQ=60)
                                                                                                |                                                                                      
TTCACATCCTGCGGGCGCGAGAGCATCAGATAATCCGTCAGGCTGGCCCAGCATGCAGAAAGCGCCACGCCGGTGAGCGCCAGCTTCATCGGCTGGTGGGTCTTTGCCAGCATCTTCAGCAATATCAACCCCGCCATGCCGCCCGCAAAGGCCAGCAGCGGCAGCACCATCACGGGCAGTGAC  >  NZ_CP009273/4501738‑4501920

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑