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
TGCGTTCAATTTCGCGTGCCAGATGTTTCTCTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAGATTTGCGCAGGCGACGAGGGCGTTGGAT  >  NZ_CP009273/384982‑385171
                                                                                                  |                                                                                           
TGCGTTCAATTTCGCGTGCCAGATGTTTCTCTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCT                                                                                            <  SRR3722079.645909/100‑1 (MQ=60)
          TTCGCGTGCCAGATGTTTCTCTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACC                                                                                  <  SRR3722079.435508/100‑1 (MQ=60)
              CGTGCCAGATGTTTCTCTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGT                                                                              <  SRR3722079.270908/100‑1 (MQ=60)
                              CTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGT                                                              <  SRR3722079.206622/100‑1 (MQ=60)
                              CTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGT                                                              >  SRR3722079.512838/1‑100 (MQ=60)
                                   ATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCT                                                         <  SRR3722079.56997/100‑1 (MQ=60)
                                       GCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCctg                                                     >  SRR3722079.580893/1‑97 (MQ=60)
                                       GCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTC                                                     >  SRR3722079.367796/1‑100 (MQ=60)
                                        CATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCA                                                    >  SRR3722079.434284/1‑100 (MQ=60)
                                             CGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACAT                                               <  SRR3722079.465771/100‑1 (MQ=60)
                                             CGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACAT                                               <  SRR3722079.769916/100‑1 (MQ=60)
                                              GCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCctgtctcttata                                              >  SRR3722079.602153/1‑88 (MQ=60)
                                                  GGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCctgtctcttatacacatctccgagccc                                          >  SRR3722079.130339/1‑73 (MQ=60)
                                                  GGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGC                                          >  SRR3722079.792884/1‑100 (MQ=60)
                                                       GGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATctgtctctta                                     >  SRR3722079.551559/1‑90 (MQ=60)
                                                       GGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGC                                     >  SRR3722079.33591/1‑100 (MQ=60)
                                                            CAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGG                                <  SRR3722079.506116/100‑1 (MQ=60)
                                                              ACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAG                              <  SRR3722079.627957/100‑1 (MQ=60)
                                                              ACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAG                              <  SRR3722079.712541/100‑1 (MQ=60)
                                                                                ATTTCTTCTTCAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAGATTTGCGCAGGCGACGAG            <  SRR3722079.483091/100‑1 (MQ=60)
                                                                                          CAACAAAGCTCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAGATTTGCGCAGGCGACGAGGGCGTTGGAT  <  SRR3722079.560988/100‑1 (MQ=60)
                                                                                                  |                                                                                           
TGCGTTCAATTTCGCGTGCCAGATGTTTCTCTGGAATGCGCATCACGCCTGGCATGGCTTCAACGGCTTTGTAGTCGTCAATTTCTTCTTCAACAAAGATCGGCAACACCAGGTCGTTAAGGCTAAGTGTTGTCTCTTCAAACATAGCGCGCAGCGCAGGAGATTTGCGCAGGCGACGAGGGCGTTGGAT  >  NZ_CP009273/384982‑385171

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: ‑