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
CGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT  >  NZ_CP009273/1854035‑1854225
                                                                                           |                                                                                                   
CGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAAC                                                                                             <  SRR3722077.428856/100‑1 (MQ=60)
  ACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGG                                                                                           <  SRR3722077.589341/100‑1 (MQ=60)
             TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAG                                                                                <  SRR3722077.122925/100‑1 (MQ=60)
             TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAG                                                                                >  SRR3722077.821165/1‑100 (MQ=60)
              TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGG                                                                               <  SRR3722077.783013/100‑1 (MQ=60)
               CCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGA                                                                              <  SRR3722077.106550/100‑1 (MQ=60)
                 ACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAA                                                                            <  SRR3722077.461920/100‑1 (MQ=60)
                  CGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAAT                                                                           >  SRR3722077.704256/1‑100 (MQ=60)
                   GATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATC                                                                          >  SRR3722077.740591/1‑100 (MQ=60)
                              GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG                                                               >  SRR3722077.308271/1‑100 (MQ=60)
                              GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG                                                               >  SRR3722077.130368/1‑100 (MQ=60)
                              GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG                                                               >  SRR3722077.1027109/1‑100 (MQ=60)
                              GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG                                                               >  SRR3722077.532308/1‑100 (MQ=60)
                                   ATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAA                                                          >  SRR3722077.30211/1‑100 (MQ=60)
                                    TATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAGAG                                                         <  SRR3722077.524097/100‑1 (MQ=60)
                                        CGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACC                                                     >  SRR3722077.177282/1‑100 (MQ=60)
                                           TGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGAC                                                  <  SRR3722077.61694/100‑1 (MQ=60)
                                                CCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCA                                             >  SRR3722077.189349/1‑100 (MQ=60)
                                                   GCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCG                                          <  SRR3722077.438008/100‑1 (MQ=60)
                                                   GCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCG                                          <  SRR3722077.590985/100‑1 (MQ=60)
                                                       ACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGC                                      <  SRR3722077.577425/100‑1 (MQ=60)
                                                        CAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCA                                     >  SRR3722077.690615/1‑100 (MQ=60)
                                                          GCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAAT                                   >  SRR3722077.1050970/1‑100 (MQ=60)
                                                          GCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAAT                                   >  SRR3722077.49403/1‑100 (MQ=60)
                                                                CCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACctgtctcttatacacatctccgagcccacgagacccacggccatctcgtatgccgtcttctgct                             >  SRR3722077.1032352/1‑36 (MQ=60)
                                                                   GTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGC                          >  SRR3722077.608095/1‑100 (MQ=60)
                                                                          TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG                   >  SRR3722077.35946/1‑100 (MQ=60)
                                                                                   AACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAAC          <  SRR3722077.319543/100‑1 (MQ=60)
                                                                                           TCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT  >  SRR3722077.995460/1‑100 (MQ=60)
                                                                                           |                                                                                                   
CGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT  >  NZ_CP009273/1854035‑1854225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑