Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273799,3250GT50.0% 25.7 / 24.9 30V123L (GTG→TTG) ybhJhydratase
Reads supporting (aligned to +/- strand):  ref base G (2/13);  new base T (15/0);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 1.75e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TAACTCACTCTGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCGGGTCAGACAGCCACA  >  NZ_CP009273/799237‑799412
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tAACTCACTCTGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTtgt                                                                                        <  1:353409/90‑1 (MQ=255)
  actcactcTGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGc                                                                                      <  2:1941379/90‑1 (MQ=255)
       ctctGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGGTTTTTTTGTCTccc                                                                                 >  1:802505/1‑89 (MQ=255)
        tctGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGc                                                                                <  1:134187/90‑1 (MQ=255)
                    gcggcACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTca                                                                    <  2:1094157/90‑1 (MQ=255)
                     cggcACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTcat                                                                   <  1:532121/90‑1 (MQ=255)
                          cTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTcatccatc                                                              <  2:1141697/90‑1 (MQ=255)
                          cTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTcatccatc                                                              <  1:1856083/90‑1 (MQ=255)
                          agaTTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTcatccatc                                                              <  1:1147166/88‑1 (MQ=255)
                                   gTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGGTTTTTTTGGCCCCCCCTATTTTGGGGCTCCCTCAATATATgg                                                     >  1:882530/1‑89 (MQ=255)
                                    tgatgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTTTGCCTCCGCATATTGCGGGCATCCATCAATATATTCg                                                    >  2:1971564/1‑90 (MQ=255)
                                    tgatgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTTTGCCTCCCCCTATTTCGGGCATCCCTCAATATATGCg                                                    >  2:644679/1‑90 (MQ=255)
                                     gatgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGATTTTTTTGCCTCCCCATATTTCGGGCATCCATCAATATATTCgg                                                   >  2:1954965/1‑89 (MQ=255)
                                      atgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGGTTTTTTTTGCTCCCCCTTTTTCGGGCCTCCCTCCATATATGGGTg                                                  >  1:376989/1‑90 (MQ=255)
                                      atgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGATTTTTTTGGCCCCGCCTATTTCGGGCATCCCTCAATATATTCggg                                                  >  2:1592264/1‑88 (MQ=255)
                                      atgaCCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGATTTTTTTGCCCCCCCCTATTTGGGGCAACCCCCAATATATggcct                                                  >  2:1147166/1‑86 (MQ=255)
                                            aTGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGGATTTTTTTGCCTCCCCATATTGCGGGCATCCCTCAATATATGCGTGGggtga                                            >  2:1563143/1‑90 (MQ=255)
                                                  ttGGTTTATCGGCGGCCCAGCGTTATGGCGGGATTTTTTTGCCCCCCCCTATTTCGGGCATCCCTCAAAATATGCGGGGGATGATGGGAg                                      >  2:1812306/1‑90 (MQ=255)
                                                                   cAGCGTTATGGCGGTATTTTTTTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGGGAGATGATGGCAGGCGGCGGCAAAAAGATc                     >  2:700424/1‑90 (MQ=255)
                                                                     gCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCt                   <  2:882530/90‑1 (MQ=255)
                                                                         tATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCggg               <  2:395686/90‑1 (MQ=255)
                                                                         tATGGCGGGATTTTTGTGCCTCCGCATATTGCGGGCATCCCTCAATATATGGGGGAGATGATGGCAGGGGGGGGCAAAAAGATCCTCcgg               >  1:340655/1‑90 (MQ=255)
                                                                          aTGGCGGTATTTTTTTGCCTCCGCATATTGCGGTCATCCATCAatata                                                        >  2:409424/1‑48 (MQ=255)
                                                                          aTGGCGGTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAatata                                                        <  1:409424/48‑1 (MQ=255)
                                                                               gggaTTTTTTTGCCTCCGCATATTGCGGGCATCCATCAATATATGCGTGGGAGGGTGGCCGGGGGGGGGAAAATGGTCCTCCGGGCAGAc         >  2:1304497/4‑90 (MQ=255)
                                                                               ggTATTTTTTTGCCTCCGCATATTTCGGTCATCCATCAAAATATGCGTGAGATGATGGCAGGGGGGGGGAAAAAGATCCCCGGGTCAGAc         >  1:1374349/1‑90 (MQ=255)
                                                                               ggTATTTTTGTGCCTCCGCCTATTGCGGGCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAAAGATTCTCGGGGCAGaa         >  2:1052722/1‑89 (MQ=255)
                                                                               ggTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCGGGTCAGAc         <  2:1584672/90‑1 (MQ=255)
                                                                               ggTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCGGGTCAGAc         <  2:1152451/90‑1 (MQ=255)
                                                                                  aTTTTTTGGCCTCCCCCTATTTCGGTCATCCATCAATATTTGCGGGGGGAGATTGAAGGGGGCGGCAAAATGATCCTCGGGTCAGagatc      >  2:1020590/1‑86 (MQ=255)
                                                                                      ttGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCGGGTCAGACAGCcaca  <  1:1052722/90‑1 (MQ=255)
                                                                                        |                                                                                       
TAACTCACTCTGCGCCGTCGGCGGCACTATTAACGGTGATGACCATGTTTTTGGTTTATCGGCGGCCCAGCGTTATGGCGGTATTTTTGTGCCTCCGCATATTGCGGTCATCCATCAATATATGCGTGAGATGATGGCAGGCGGCGGCAAAATGATCCTCGGGTCAGACAGCCACA  >  NZ_CP009273/799237‑799412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑