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
ATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG  >  NZ_CP009273/2982465‑2982651
                                                                                          |                                                                                                
ATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGC                                                                                         >  SRR3722077.586596/1‑100 (MQ=60)
            GGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACC                                                                             >  SRR3722077.899382/1‑100 (MQ=60)
            GGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACC                                                                             >  SRR3722077.1130902/1‑100 (MQ=60)
                             AAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGG                                                            <  SRR3722077.871396/100‑1 (MQ=60)
                             AAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGG                                                            <  SRR3722077.365612/100‑1 (MQ=60)
                             AAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGG                                                            <  SRR3722077.692594/100‑1 (MQ=60)
                               ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA                                                          >  SRR3722077.166766/1‑100 (MQ=60)
                                    AAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAA                                                     >  SRR3722077.743116/1‑100 (MQ=60)
                                           agacagGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAAC                                              <  SRR3722077.424226/94‑1 (MQ=60)
                                                  GATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACC                                       <  SRR3722077.180956/100‑1 (MQ=60)
                                                        GGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATG                                 >  SRR3722077.857613/1‑100 (MQ=60)
                                                                CTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGctgtc                         >  SRR3722077.779311/1‑95 (MQ=60)
                                                                  GTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAA                       >  SRR3722077.793135/1‑100 (MQ=60)
                                                                           ATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAC              <  SRR3722077.439471/100‑1 (MQ=60)
                                                                             CCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC            <  SRR3722077.770585/100‑1 (MQ=60)
                                                                             CCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC            <  SRR3722077.1104714/100‑1 (MQ=60)
                                                                               GTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCActgtctcttatacacatctccgagcccacgagacccacggccatctcg          >  SRR3722077.428928/1‑52 (MQ=60)
                                                                               GNGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCActgtctcttatacacatctccgagcccacgagacccacggccatctcg          >  SRR3722077.251676/1‑52 (MQ=60)
                                                                                  GTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCT       >  SRR3722077.972126/1‑100 (MQ=60)
                                                                                     ATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTAC    <  SRR3722077.137740/100‑1 (MQ=60)
                                                                                     ATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTAC    <  SRR3722077.1088627/100‑1 (MQ=60)
                                                                                       ACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG  <  SRR3722077.283342/100‑1 (MQ=60)
                                                                                          |                                                                                                
ATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG  >  NZ_CP009273/2982465‑2982651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑