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
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT  >  NZ_CP009273/2202073‑2202263
                                                                                                  |                                                                                            
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGC                                                                                             >  SRR3722077.70429/1‑100 (MQ=60)
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCC                                                                                             >  SRR3722077.720507/1‑100 (MQ=60)
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCC                                                                                             <  SRR3722077.18267/100‑1 (MQ=60)
              ATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATT                                                                               >  SRR3722077.99375/1‑100 (MQ=60)
                        GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCctgtctcttatacaca                                                                     >  SRR3722077.71373/1‑84 (MQ=60)
                        GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATC                                                                     >  SRR3722077.185608/1‑100 (MQ=60)
                        GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATC                                                                     >  SRR3722077.23402/1‑100 (MQ=60)
                                    GATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTG                                                         >  SRR3722077.695874/1‑100 (MQ=60)
                                     ATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCctgtctcttatacacatctccgagcccac                                                        >  SRR3722077.684495/1‑71 (MQ=60)
                                      TCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGAC                                                       <  SRR3722077.1115678/100‑1 (MQ=60)
                                                   ATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTG                                          <  SRR3722077.1058589/100‑1 (MQ=60)
                                                                  gagacagCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACG                           <  SRR3722077.252099/93‑1 (MQ=60)
                                                                      ACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGC                       >  SRR3722077.273874/1‑100 (MQ=60)
                                                                      ACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGC                       >  SRR3722077.163495/1‑100 (MQ=60)
                                                                                 ATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAG            <  SRR3722077.395782/100‑1 (MQ=60)
                                                                                         CTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTA    <  SRR3722077.655912/100‑1 (MQ=60)
                                                                                           GTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT  >  SRR3722077.1117032/1‑100 (MQ=60)
                                                                                                  |                                                                                            
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT  >  NZ_CP009273/2202073‑2202263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑