Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9180AC37.2% 61.7 / 17.7 43intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base A (24/3);  new base C (0/16);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 3.65e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001783‑2002051
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aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑cccc                                                                                                                                   >  1:599399/1‑140 (MQ=255)
 aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCccg                                                                                                                                  >  1:997427/1‑140 (MQ=255)
   tCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCccgcc                                                                                                                                >  1:55122/1‑140 (MQ=255)
    cACGATAAACGGCCCTGCTTTATATGAGTTATCGGCATGATTATCCTTTTCTGCAGGTTTTTTAATCGGACGATTAGGGGGTGAAAGGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAAAAAAAAC‑CCccgccg                                                                                                                               <  2:138862/140‑1 (MQ=255)
                          tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTg                                                                                                         >  2:1271418/1‑140 (MQ=255)
                          tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTg                                                                                                         >  1:768618/1‑140 (MQ=255)
                               gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:1503517/1‑140 (MQ=255)
                               gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:243213/1‑140 (MQ=255)
                                 tATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                  >  2:1376213/1‑140 (MQ=255)
                                 tATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                  >  1:1377643/1‑140 (MQ=255)
                                    gggCATGATTATCCTTTTCTGCAGGTTTTTTAATCGGACGATTAGTGGGTGAAATGGGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                               <  2:455404/139‑1 (MQ=255)
                                    cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                               >  2:668028/1‑140 (MQ=255)
                                    cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                               >  1:73728/1‑140 (MQ=255)
                                     ggCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcgc                                                                                              >  1:282845/1‑140 (MQ=255)
                                        aTGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt                                                                                           >  1:1006042/1‑140 (MQ=255)
                                          gATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAt                                                                                         >  1:593686/1‑140 (MQ=255)
                                          gATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAt                                                                                         >  2:938054/1‑140 (MQ=255)
                                           tttATCCTTTTCTGCGGGTTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTATTGGGGGG‑TTACAGGTAAATTCCAGGAAAAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATg                                                                                        <  2:599399/139‑1 (MQ=255)
                                           aTTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTATTGGGGGG‑TTACAGGTAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATg                                                                                        <  1:52637/140‑1 (MQ=255)
                                             tttCCTTTTCTGCGGGTTTTTTAATCGGACGATTGGGGGGTAAAATG‑GGGGTTTTTTGGGGGTTTACAGGTAAATCCCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGtt                                                                                      <  2:768618/138‑1 (MQ=255)
                                                       tGCAGGGTTTTTAATGGGACGATTAGTGGGTAAAATGAGGGTTTTTTTGGGGG‑TTAAAGGAAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcg                                                                            <  2:1006042/140‑1 (MQ=255)
                                                        gCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGCTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcgg                                                                           >  1:743569/1‑140 (MQ=255)
                                                             gTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      >  1:1155755/1‑140 (MQ=255)
                                                             gTTTTTAATCGGACGATTAGGGGGTGAAATGGGGGGTTTTTTGGGGT‑TTACAGGAAAATTCCGGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      <  1:1010107/140‑1 (MQ=255)
                                                                      gggACGATTAGGGGGTAAAATGGGGGGTTATTGGGGGG‑TTAAAGGTAAATCCCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTAt                                                             <  2:73728/139‑1 (MQ=255)
                                                                       ggACGATTAGTGGGTGAAATGAGGGGTTATTGGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATc                                                            <  1:55366/140‑1 (MQ=255)
                                                                        gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                           >  1:1008134/1‑140 (MQ=255)
                                                                           gATTGGTGGGTAAAATGAGGGGTTTTTGGGGGG‑TTACAGTTAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGc                                                        <  2:1008134/140‑1 (MQ=38)
                                                                                   ggTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                >  2:774921/1‑140 (MQ=255)
                                                                                          ggAGGGGTTATTGGGGGT‑TTACAGGAAAATTCCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCa                                         <  2:1155755/139‑1 (MQ=38)
                                                                                            gggggTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCaaa                                       <  2:282845/139‑1 (MQ=255)
                                                                                              gggTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAtt                                     >  1:837970/1‑140 (MQ=255)
                                                                                                  tATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAAt                                 >  1:962710/1‑140 (MQ=255)
                                                                                                   ttttGGGGG‑TTACAGGAAAATCCCAGGAAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                <  2:55122/139‑1 (MQ=255)
                                                                                                               aCAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  2:907059/1‑140 (MQ=255)
                                                                                                               aCAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  2:60570/1‑140 (MQ=255)
                                                                                                               aCAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  1:1534302/1‑140 (MQ=255)
                                                                                                               aCAGGTAAATTCCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     <  2:927481/140‑1 (MQ=255)
                                                                                                                     aaaTTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg               <  1:774921/140‑1 (MQ=255)
                                                                                                                     aaaTCCCAGGAAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg               <  2:243213/140‑1 (MQ=255)
                                                                                                                       aTTCCAGGCAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa             <  2:1503517/140‑1 (MQ=255)
                                                                                                                        atCCCGGCAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa             <  1:354863/139‑1 (MQ=255)
                                                                                                                          ccAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc          <  1:1376213/140‑1 (MQ=255)
                                                                                                                                  aaaaaaa‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAag  >  1:1527713/1‑140 (MQ=255)
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AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001783‑2002051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑