Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9180AC37.5% 51.9 / 21.1 40intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base A (23/2);  new base C (0/15);  total (23/17)
Fisher's exact test for biased strand distribution p-value = 3.38e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001779‑2002051
                                                                                                                                            |                                                                                                                                     
agTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGaaaaaaa                                                                                                                                       >  1:3268/1‑140 (MQ=255)
  tGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAAcc                                                                                                                                     >  2:714647/1‑140 (MQ=255)
    aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAAcccc                                                                                                                                   >  1:1004688/1‑140 (MQ=255)
    aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAAcccc                                                                                                                                   >  2:335511/1‑140 (MQ=255)
                    cccTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAg                                                                                                                   <  1:488647/140‑1 (MQ=255)
                       tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCAc                                                                                                                >  1:909097/1‑140 (MQ=255)
                       tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCAc                                                                                                                >  1:560833/1‑140 (MQ=255)
                              tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTg                                                                                                         >  1:1176470/1‑140 (MQ=255)
                              tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTg                                                                                                         >  1:639524/1‑140 (MQ=255)
                                   gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:298303/1‑140 (MQ=255)
                                     taccGGAATGATTATCCGTTTCTGCGGGTTTTTTAATCGGACGTTTGGTGGGTAAAAGGGGGGGTTATTG‑GGGGGTTACAGTTAAACCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                  <  2:639524/137‑1 (MQ=255)
                                     tATCGGCATGATTATCCGTTTCTGCAGGTTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTATTG‑GGGGGTTAAAGGAAAATTCCAGGCAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                  <  1:922697/140‑1 (MQ=255)
                                      aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                 >  2:308807/1‑140 (MQ=255)
                                          gCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCt                                                                                             >  2:453561/1‑140 (MQ=255)
                                                        ttCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt                                                                               >  1:580083/1‑140 (MQ=255)
                                                        ttCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt                                                                               >  1:796137/1‑140 (MQ=255)
                                                          cTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgc                                                                             >  1:583487/1‑140 (MQ=255)
                                                          cTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgc                                                                             >  1:253968/1‑140 (MQ=255)
                                                           tGCGGGTTTTTTAATCGGACGATTAGGGGGTAAAATGGGGGTTTTTTG‑GGGGGTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcg                                                                            <  2:253968/140‑1 (MQ=255)
                                                              aGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggcg                                                                         >  2:23080/1‑140 (MQ=255)
                                                                 tttttaAATCGGACGATTGGGGGGTAAAAGGGGGGGTTATTG‑GGGGGTTACAGGTAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      <  2:3268/139‑1 (MQ=255)
                                                                          gggACGATTAGTGGGTGAAAGGAGGGGTTTTTG‑GGGGGTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTAt                                                             <  2:560833/139‑1 (MQ=255)
                                                                           ggACGATTGGGGGGTGAAATGGGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATc                                                            <  2:1303738/140‑1 (MQ=39)
                                                                                aTTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGcc                                                       >  1:923978/1‑140 (MQ=255)
                                                                                             aTGGGGGTTTATTG‑GGGGGTTACAGTTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                          <  2:298303/140‑1 (MQ=37)
                                                                                                   ggTTTTTTGGGGGGTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAtt                                     <  2:583487/140‑1 (MQ=38)
                                                                                                             gggtTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTACAAATTCAATAAATTg                           <  2:1004688/140‑1 (MQ=37)
                                                                                                              gggTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGc                          >  2:908861/1‑140 (MQ=255)
                                                                                                                gTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa                        >  1:314283/1‑140 (MQ=255)
                                                                                                                gTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa                        >  2:910325/1‑140 (MQ=255)
                                                                                                                gTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa                        >  1:677737/1‑140 (MQ=255)
                                                                                                                   aCAGGTAAATTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     <  1:23080/140‑1 (MQ=255)
                                                                                                                   aCAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  2:1289544/1‑140 (MQ=255)
                                                                                                                   aCAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     <  2:796137/140‑1 (MQ=37)
                                                                                                                    cAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                    <  2:1019500/140‑1 (MQ=255)
                                                                                                                    aaGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                    <  2:923978/139‑1 (MQ=255)
                                                                                                                         aaaTTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg               <  1:908861/140‑1 (MQ=255)
                                                                                                                          aaTTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCa                         >  2:1159069/1‑129 (MQ=255)
                                                                                                                          aaTTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCa                         <  1:1159069/129‑1 (MQ=255)
                                                                                                                          aaTTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGt              >  2:919231/1‑140 (MQ=255)
                                                                                                                           atcccAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGTGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa             <  1:622633/137‑1 (MQ=255)
                                                                                                                              ccAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc          <  1:1405343/140‑1 (MQ=255)
                                                                                                                                      aaaaaaaCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAag  <  1:919231/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                     
AGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001779‑2002051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑