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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAAC  >  NZ_CP009273/2554023‑2554218
                                                                                                  |                                                                                                 
aagacggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacaGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACC                                                                                                  <  SRR3722077.279514/42‑1 (MQ=60)
    CTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGG                                                                                              >  SRR3722077.199737/1‑100 (MQ=60)
        GTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAA                                                                                          >  SRR3722077.966251/1‑100 (MQ=60)
            CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAA                                                                                      <  SRR3722077.791494/100‑1 (MQ=60)
            CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAA                                                                                      <  SRR3722077.300931/100‑1 (MQ=60)
                   GGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCG                                                                               >  SRR3722077.837941/1‑100 (MQ=60)
                         GGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTC                                                                         >  SRR3722077.176932/1‑100 (MQ=60)
                                            GATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACT                                                      <  SRR3722077.310948/100‑1 (MQ=60)
                                                GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT                                                  >  SRR3722077.919214/1‑100 (MQ=60)
                                                GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT                                                  >  SRR3722077.577015/1‑100 (MQ=60)
                                                GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT                                                  >  SRR3722077.632131/1‑100 (MQ=60)
                                                 TGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTG                                                 <  SRR3722077.515127/100‑1 (MQ=60)
                                                 TGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTG                                                 <  SRR3722077.63451/100‑1 (MQ=60)
                                                       GTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTA                                           >  SRR3722077.424022/1‑100 (MQ=60)
                                                          GGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTG                                        <  SRR3722077.949433/100‑1 (MQ=60)
                                                           GTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGA                                       >  SRR3722077.228687/1‑100 (MQ=60)
                                                                    CAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATAT                              <  SRR3722077.217569/100‑1 (MQ=60)
                                                                      ATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATAC                            <  SRR3722077.75317/100‑1 (MQ=60)
                                                                       TCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACC                           <  SRR3722077.879323/100‑1 (MQ=60)
                                                                         GACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAG                         <  SRR3722077.140733/100‑1 (MQ=60)
                                                                                     AGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAA             >  SRR3722077.725914/1‑100 (MQ=60)
                                                                                     AGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAA             >  SRR3722077.248669/1‑100 (MQ=60)
                                                                                      GGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAG            >  SRR3722077.295962/1‑100 (MQ=60)
                                                                                          ATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCtgtctcttataca        >  SRR3722077.46811/1‑87 (MQ=60)
                                                                                          ATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAG        >  SRR3722077.41144/1‑100 (MQ=60)
                                                                                                AAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAAC  <  SRR3722077.458657/100‑1 (MQ=60)
                                                                                                  |                                                                                                 
TGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAAC  >  NZ_CP009273/2554023‑2554218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑