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
ATCTCCAGCAGGCCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  >  NZ_CP009273/2882314‑2882506
                                                                                                    |                                                                                             
ATCTCCAGCAGGCCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAA                                                                                               >  SRR3722077.1045507/1‑100 (MQ=60)
 TCTCCAGCAGGCCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACC                                                                                              <  SRR3722077.799131/100‑1 (MQ=60)
  CTCCAGCAGGCCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCC                                                                                             >  SRR3722077.718111/1‑100 (MQ=60)
            CCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATAC                                                                                   <  SRR3722077.76496/100‑1 (MQ=60)
                    CAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCT                                                                           <  SRR3722077.1142462/100‑1 (MQ=60)
                       CGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGT                                                                        >  SRR3722077.1033549/1‑100 (MQ=60)
                                CGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAAC                                                               <  SRR3722077.257907/100‑1 (MQ=60)
                                       TCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCGTATG                                                        <  SRR3722077.1121712/100‑1 (MQ=60)
                                          AGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGAC                                                     <  SRR3722077.1010433/100‑1 (MQ=60)
                                                    CATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTC                                           <  SRR3722077.316301/100‑1 (MQ=60)
                                                     ATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACctgtctcttat                                          >  SRR3722077.9885/1‑89 (MQ=60)
                                                         TCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATT                                      <  SRR3722077.661825/100‑1 (MQ=60)
                                                         TCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATT                                      <  SRR3722077.750329/100‑1 (MQ=60)
                                                         TCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATT                                      <  SRR3722077.1162562/100‑1 (MQ=60)
                                                         TCAATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATT                                      <  SRR3722077.124960/100‑1 (MQ=60)
                                                                 CAGCGTCAGGTGCCAGTTATCATCAATGCCCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCC                               <  SRR3722077.896607/100‑1 (MQ=60)
                                                                        AGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGAC                       <  SRR3722077.108650/100‑1 (MQ=60)
                                                                          GTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGC                     >  SRR3722077.260037/1‑100 (MQ=60)
                                                                            GCCAGTTATCATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTC                   <  SRR3722077.562693/100‑1 (MQ=60)
                                                                                GTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACT               >  SRR3722077.1127767/1‑100 (MQ=60)
                                                                                     CATCAATG‑CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGC          >  SRR3722077.387210/1‑100 (MQ=60)
                                                                                              CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACTCTCCACTTCCGCTgtctctt  >  SRR3722077.65806/1‑93 (MQ=60)
                                                                                              CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  >  SRR3722077.654807/1‑100 (MQ=60)
                                                                                              CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  <  SRR3722077.700030/100‑1 (MQ=60)
                                                                                              CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  >  SRR3722077.1137901/1‑100 (MQ=60)
                                                                                              CCCTTACCCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  >  SRR3722077.892255/1‑100 (MQ=60)
                                                                                                    |                                                                                             
ATCTCCAGCAGGCCGGTTTTCAGCGGACGCGCCGGATAATCAAGGATGCGACCATTTTCGATAAACAGCGTCAGGTGCCAGTTATCATCAATG‑CCCTTAACCCAGCCAATACGATCGCCTCGTCCGGTGAACTCATATGGACGGATCGGTTCAAATTTGATCCCCGCGCGACGCTCCACTTCCGCTTTAAACG  >  NZ_CP009273/2882314‑2882506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑