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
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACCTGGC  >  NZ_CP009273/4211082‑4211267
                                                                                        |                                                                                                 
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCC                                                                                       <  SRR3722077.695510/100‑1 (MQ=60)
 agTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCC                                                                                       <  SRR3722077.889244/98‑1 (MQ=60)
  ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCT                                                                                      >  SRR3722077.1112410/1‑100 (MQ=60)
  ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTT                                                                                     <  SRR3722077.837196/100‑1 (MQ=60)
       TATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATAT                                                                                <  SRR3722077.754321/100‑1 (MQ=60)
        ATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATC                                                                               >  SRR3722077.1158226/1‑100 (MQ=60)
         TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATC                                                                               <  SRR3722077.4621/100‑1 (MQ=60)
         TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCC                                                                              <  SRR3722077.137808/100‑1 (MQ=60)
         TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCC                                                                              <  SRR3722077.484460/100‑1 (MQ=60)
          agatgtgtataagagacagAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCC                                                                              <  SRR3722077.135912/81‑1 (MQ=60)
            TTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTG                                                                            <  SRR3722077.1150795/100‑1 (MQ=60)
              ACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTT                                                                          >  SRR3722077.428527/1‑100 (MQ=60)
                          cagAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAAT                                                             <  SRR3722077.458178/97‑1 (MQ=60)
                               ATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAA                                                        <  SRR3722077.1097571/100‑1 (MQ=60)
                                 AATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAA                                                       <  SRR3722077.942565/100‑1 (MQ=60)
                                     CAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTC                                                  >  SRR3722077.802239/1‑100 (MQ=60)
                                                  TTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCC                                      <  SRR3722077.484606/100‑1 (MQ=60)
                                                  TTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCC                                      <  SRR3722077.565460/100‑1 (MQ=60)
                                                                   GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA                    >  SRR3722077.1073859/1‑100 (MQ=60)
                                                                   GAATATGCATGAGA‑TTTTCTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA                    >  SRR3722077.15594/1‑100 (MQ=60)
                                                                       ATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCC                 <  SRR3722077.334211/100‑1 (MQ=60)
                                                                            TGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATAT           <  SRR3722077.519957/100‑1 (MQ=60)
                                                                                      TTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACCTGGC  >  SRR3722077.21673/1‑100 (MQ=60)
                                                                                        |                                                                                                 
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACCTGGC  >  NZ_CP009273/4211082‑4211267

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑