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 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCAAG  >  NZ_CP009273/4057780‑4057969
                                                                                             |                                                                                                
ctctctggtctcgtgggctcggagatgtgtataagagacagGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATA                                                                                            <  SRR3722079.804124/59‑1 (MQ=60)
GTTGATTCCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATA                                                                                            <  SRR3722079.278036/100‑1 (MQ=60)
        CCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAG                                                                                    >  SRR3722079.528472/1‑100 (MQ=60)
               AATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGC                                                                             >  SRR3722079.684291/1‑100 (MQ=60)
               AATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGATGACGC                                                                             <  SRR3722079.169112/100‑1 (MQ=60)
                   AATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAAC                                                                         <  SRR3722079.334708/100‑1 (MQ=60)
                    ATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACC                                                                        >  SRR3722079.59486/1‑100 (MQ=60)
                          atgtgtataagagacagGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAA                                                                  <  SRR3722079.351377/83‑1 (MQ=60)
                             GTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGT                                                               <  SRR3722079.783009/100‑1 (MQ=60)
                             GTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGT                                                               >  SRR3722079.833009/1‑100 (MQ=60)
                                  TCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCAT                                                          <  SRR3722079.718101/100‑1 (MQ=60)
                                         GTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTG                                                   >  SRR3722079.116598/1‑100 (MQ=60)
                                           GTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCG                                                 >  SRR3722079.14960/1‑100 (MQ=60)
                                           GTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCG                                                 >  SRR3722079.446851/1‑100 (MQ=60)
                                                   GAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTctgtctcttatacacatctccgagccc                                         >  SRR3722079.269335/1‑73 (MQ=60)
                                                      TCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGA                                      <  SRR3722079.371026/100‑1 (MQ=60)
                                                      TCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGA                                      <  SRR3722079.158059/100‑1 (MQ=60)
                                                        CCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAAC                                    <  SRR3722079.290693/100‑1 (MQ=60)
                                                        CCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAAC                                    <  SRR3722079.153892/100‑1 (MQ=60)
                                                              TCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACC                              >  SRR3722079.528565/1‑100 (MQ=60)
                                                                         ATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCA                   >  SRR3722079.698827/1‑100 (MQ=60)
                                                                         ATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCA                   >  SRR3722079.132016/1‑100 (MQ=60)
                                                                                CCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAAT            >  SRR3722079.85159/1‑100 (MQ=60)
                                                                                  AGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGC          <  SRR3722079.225010/100‑1 (MQ=60)
                                                                                   GTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCtgtctcttatacacatctccgagcccacgagaccagagaggatctcgtatgcc         >  SRR3722079.405362/1‑47 (MQ=60)
                                                                                   GTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCC         >  SRR3722079.504530/1‑100 (MQ=60)
                                                                                     GCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTG       >  SRR3722079.347209/1‑100 (MQ=60)
                                                                                          AGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCTAG  >  SRR3722079.99556/1‑100 (MQ=60)
                                                                                             |                                                                                                
GTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCAAG  >  NZ_CP009273/4057780‑4057969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑