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 F1 I191 R1 4 28.5 1785710 94.7% 1691067 84.1

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCATTGAACTTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGCTGA  >  NZ_CP009273/886650‑886829
                                                                                          |                                                                                         
CCATTGAACTTATTTGTGGCCATCGCTCCATTCGCCATTTCAGTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGAC                                                                                  >  SRR3722068.24457/1‑100 (MQ=60)
       ACTTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGT                                                                           >  SRR3722068.736191/1‑100 (MQ=60)
         TTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTC                                                                         <  SRR3722068.57795/100‑1 (MQ=60)
                   CCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTG                                                               >  SRR3722068.371000/1‑100 (MQ=60)
                    ccaccgagatctacaccgcggttatcgtcggcagcgtcagatgtgtataagagacaGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGC                                                              <  SRR3722068.271914/44‑1 (MQ=60)
                        GCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTG                                                          >  SRR3722068.60533/1‑100 (MQ=60)
                                 GCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCAT                                                 <  SRR3722068.4937/100‑1 (MQ=60)
                                   CATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTA                                               <  SRR3722068.69736/100‑1 (MQ=60)
                                       TCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCG                                           >  SRR3722068.83583/1‑100 (MQ=60)
                                            GATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCActg                                      >  SRR3722068.744964/1‑97 (MQ=60)
                                               GAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCG                                   >  SRR3722068.737779/1‑100 (MQ=60)
                                                              GCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTG                    >  SRR3722068.877751/1‑100 (MQ=60)
                                                                   GCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAA               >  SRR3722068.47896/1‑100 (MQ=60)
                                                                             ATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGC     >  SRR3722068.589558/1‑100 (MQ=60)
                                                                             ATTATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGC     >  SRR3722068.103081/1‑100 (MQ=60)
                                                                               TATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGCTG   >  SRR3722068.191506/1‑100 (MQ=60)
                                                                                ATTAACAGCGGCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCctgtctcttatacacatctgacgctgccgacgataaccgcgg  >  SRR3722068.356381/1‑58 (MQ=60)
                                                                                          |                                                                                         
CCATTGAACTTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGCTGA  >  NZ_CP009273/886650‑886829

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: ‑