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
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTCGGCAATTTTCTT  >  NZ_CP009273/1965683‑1965880
                                                                                                   |                                                                                                  
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGG                                                                                                    >  SRR3722077.24897/1‑100 (MQ=60)
       TCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCG                                                                                             <  SRR3722077.416344/100‑1 (MQ=60)
               GGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCG                                                                                     >  SRR3722077.784764/1‑100 (MQ=60)
                  TTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCT                                                                                  <  SRR3722077.187363/100‑1 (MQ=60)
                     GATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCA                                                                               >  SRR3722077.28557/1‑100 (MQ=60)
                        CTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACC                                                                            <  SRR3722077.925716/100‑1 (MQ=60)
                                 CGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTC                                                                   <  SRR3722077.1053493/100‑1 (MQ=60)
                                 CGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTC                                                                   <  SRR3722077.441391/100‑1 (MQ=60)
                                         CGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCtgtctcttatacacatctccgagcccacgagac                                                           >  SRR3722077.844201/1‑67 (MQ=60)
                                                 CTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAG                                                   <  SRR3722077.555086/100‑1 (MQ=60)
                                                   GGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTC                                                 <  SRR3722077.723826/100‑1 (MQ=60)
                                                        GATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAA                                            >  SRR3722077.322719/1‑100 (MQ=60)
                                                        GATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAA                                            <  SRR3722077.1084544/100‑1 (MQ=60)
                                                         ATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAG                                           >  SRR3722077.1106133/1‑100 (MQ=60)
                                                                gtctcgtgggctcggagatgtgtataagagacagGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC                                    <  SRR3722077.154132/66‑1 (MQ=60)
                                                                CCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC                                    <  SRR3722077.1162130/100‑1 (MQ=60)
                                                                ACTCCCCCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC                                    <  SRR3722077.752354/100‑1 (MQ=60)
                                                                       CCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGAT                             <  SRR3722077.125459/100‑1 (MQ=60)
                                                                                  GCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAA                  <  SRR3722077.611329/100‑1 (MQ=60)
                                                                                  GCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAA                  >  SRR3722077.864413/1‑100 (MQ=60)
                                                                                               CCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTCGGCAATTTT     >  SRR3722077.177233/1‑100 (MQ=60)
                                                                                                  GGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTCGGCAATTTTCTT  >  SRR3722077.434346/1‑100 (MQ=60)
                                                                                                   |                                                                                                  
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTCGGCAATTTTCTT  >  NZ_CP009273/1965683‑1965880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑