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 I228 R1 214 26.5 1448192 97.1% 1406194 86.4

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AAATGAGGATAACCGGATGAAAAAATGGGCAGTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGTAACGCGATGC  >  NZ_CP009273/2964614‑2964807
                                                                                              |                                                                                                   
AAATGAGGATAACCGGATGAAAAAATGGGCAGTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGCCGACC                                                                                                <  SRR3722112.265853/100‑1 (MQ=60)
      GGATAACCGGATGAAAAAATGGGCAGTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGCCGACCAAAGAT                                                                                          >  SRR3722112.83777/1‑100 (MQ=60)
                               GTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAA                                                                 >  SRR3722112.508210/1‑100 (MQ=60)
                               GTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAA                                                                 >  SRR3722112.508168/1‑100 (MQ=60)
                                                     TGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATAC                                           <  SRR3722112.471355/100‑1 (MQ=60)
                                                      GGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACC                                          <  SRR3722112.314095/100‑1 (MQ=60)
                                                                  TTCCGGGTGTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGT                              <  SRR3722112.1980/100‑1 (MQ=60)
                                                                        GTGTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCAC                        >  SRR3722112.628517/1‑100 (MQ=60)
                                                                         TGTTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACG                       <  SRR3722112.253421/100‑1 (MQ=60)
                                                                          GTTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGA                      <  SRR3722112.479079/100‑1 (MQ=60)
                                                                          GTTCCAGTGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGA                      >  SRR3722112.465114/1‑100 (MQ=60)
                                                                           TTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGAT                     >  SRR3722112.281349/1‑100 (MQ=60)
                                                                                 TGATTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAA               >  SRR3722112.522361/1‑100 (MQ=60)
                                                                                   ATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGG             <  SRR3722112.361483/100‑1 (MQ=60)
                                                                                    TTACGTCATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGT            <  SRR3722112.485412/100‑1 (MQ=60)
                                                                                      ACGTGATGCCGACCAAAGATGGCCGTATGATTTTGACCGAGGGAAAGCCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGTAA          <  SRR3722112.448881/100‑1 (MQ=60)
                                                                                           ATGCCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGTAACGCGA     <  SRR3722112.271711/100‑1 (MQ=60)
                                                                                              GCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGTAACGCGATGC  <  SRR3722112.47918/100‑1 (MQ=60)
                                                                                              |                                                                                                   
AAATGAGGATAACCGGATGAAAAAATGGGCAGTAATAATTTCTGCAGTCGGACTGGCGTTTGCTGTTTCCGGGTGTTCCAGTGATTACGTCATGGCGACCAAAGATGGCCGTATGATTTTGACCGATGGAAAACCTGAAATTGATGATGATACCGGGCTGGTGAGTTATCACGATCAGCAAGGTAACGCGATGC  >  NZ_CP009273/2964614‑2964807

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑