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
TTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATTGCG  >  NZ_CP009273/2726468‑2726660
                                                                                              |                                                                                                  
TTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGT                                                                                              <  SRR3722077.546015/100‑1 (MQ=60)
  CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTAC                                                                                            >  SRR3722077.1143157/1‑100 (MQ=60)
  CTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTAC                                                                                            <  SRR3722077.894520/100‑1 (MQ=60)
     TCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGG                                                                                         <  SRR3722077.583674/100‑1 (MQ=60)
            ACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATAT                                                                                   <  SRR3722077.184232/100‑1 (MQ=60)
             CGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATT                                                                                  >  SRR3722077.446650/1‑100 (MQ=60)
                 GAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCA                                                                             >  SRR3722077.302860/1‑100 (MQ=60)
                     acgagatggccgtgggtctcgtgggctcggagatgtgtataagagacagCGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCG                                                                         <  SRR3722077.806380/51‑1 (MQ=60)
                                CTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCT                                                              >  SRR3722077.359668/1‑100 (MQ=60)
                                    AACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGC                                                          <  SRR3722077.288756/100‑1 (MQ=60)
                                     ACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGC                                                          <  SRR3722077.899726/100‑1 (MQ=60)
                                     ACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCA                                                         >  SRR3722077.112851/1‑100 (MQ=60)
                                                 GCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATC‑TTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACC                                             >  SRR3722077.809240/1‑100 (MQ=60)
                                                                             CCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTT                  >  SRR3722077.466123/1‑100 (MQ=60)
                                                                                  acaggcatcTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGG             <  SRR3722077.533539/91‑1 (MQ=60)
                                                                                        TCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCA       >  SRR3722077.880541/1‑100 (MQ=60)
                                                                                         CTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCAT      <  SRR3722077.836203/100‑1 (MQ=60)
                                                                                          CTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATT     >  SRR3722077.385033/1‑100 (MQ=60)
                                                                                             TTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATTGCG  >  SRR3722077.8097/1‑100 (MQ=60)
                                                                                              |                                                                                                  
TTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCGATATTCGTCAAGCGTCGTGGCACCTACGCAGTGCAATTCACCACGCGCCAGCGCCGGTTTCAGCATGTTTCCGGCGTCCATTGCG  >  NZ_CP009273/2726468‑2726660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑