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
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA  >  NZ_CP009273/4215629‑4215823
                                                                                               |                                                                                                   
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGA                                                                                                 <  SRR3722077.367420/100‑1 (MQ=60)
       CACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAAT                                                                                          <  SRR3722077.2745/100‑1 (MQ=60)
          CGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAA                                                                                       <  SRR3722077.291987/100‑1 (MQ=60)
           GAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAAC                                                                                      <  SRR3722077.1051887/100‑1 (MQ=60)
                 gggtctcgtgggctcggagatgtgtataagagacagACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGG                                                                                <  SRR3722077.891491/64‑1 (MQ=60)
                   ACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAA                                                                              <  SRR3722077.820251/100‑1 (MQ=60)
                      GGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATAC                                                                           <  SRR3722077.958126/100‑1 (MQ=60)
                      GGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATAC                                                                           >  SRR3722077.31598/1‑100 (MQ=60)
                        AGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTC                                                                         <  SRR3722077.276889/100‑1 (MQ=60)
                        AGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTC                                                                         <  SRR3722077.394591/100‑1 (MQ=60)
                                    AATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGG                                                             <  SRR3722077.850468/100‑1 (MQ=60)
                                            cggagatgtgtataagagacaGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCG                                                     <  SRR3722077.942854/79‑1 (MQ=60)
                                                            ACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGA                                     >  SRR3722077.289206/1‑100 (MQ=60)
                                                             CACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGAT                                    <  SRR3722077.873103/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               <  SRR3722077.1004100/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               <  SRR3722077.571653/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               <  SRR3722077.741871/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               <  SRR3722077.967130/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               <  SRR3722077.31416/100‑1 (MQ=60)
                                                                  CCAACGCCCAGCAGGCGGAGTGCCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA                               >  SRR3722077.12384/1‑100 (MQ=60)
                                                                      CGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAA                           >  SRR3722077.1081244/1‑100 (MQ=60)
                                                                             CAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCC                    >  SRR3722077.299938/1‑100 (MQ=60)
                                                                                    AGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGC             <  SRR3722077.1056603/100‑1 (MQ=60)
                                                                                           CTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGC      >  SRR3722077.598411/1‑100 (MQ=60)
                                                                                               GGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA  >  SRR3722077.1140206/1‑100 (MQ=60)
                                                                                               |                                                                                                   
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA  >  NZ_CP009273/4215629‑4215823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑