Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,544,0211.A74.4% 101.7 / 31.8 39coding (40/1389 nt)narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (7/3);  new base A (14/15);  total (21/18)
Fisher's exact test for biased strand distribution p-value = 2.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTTTATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGG  >  NC_000913_3_pae_tpiA/1543874‑1544153
                                                                                                                                                     |                                                                                                                                      
gtttATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTcgc‑ga                                                                                                                                        <  1:556377/148‑2 (MQ=255)
    aTTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aa‑aa                                                                                                                                 <  2:1231655/149‑1 (MQ=255)
                       gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATACCGACTATTTTtct                                                                                                               >  2:1273142/1‑149 (MQ=255)
                         gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGG‑A‑AA‑AAGATAACGACTATTTTTCTCa                                                                                                             >  1:1188570/1‑149 (MQ=255)
                               tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGc                                                                                                       >  2:168131/1‑149 (MQ=255)
                                   aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                   >  2:937538/1‑149 (MQ=255)
                                       aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCat                                                                                               >  2:382176/1‑149 (MQ=255)
                                             aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                  >  2:996155/1‑140 (MQ=255)
                                             aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                  <  1:996155/140‑1 (MQ=255)
                                                  gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGGGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                    >  2:854786/1‑149 (MQ=255)
                                                   cAAGCAGTGGACAGCTGACTGTGATCTAGAGTTTTCCTCTAGCAACTTTGTTTCCTTTATTTTCCCAGAAGGCCGGATGGTCTGTTTTCCAGTCGC‑G‑A‑AATAAGATAACGACTGTTGTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                   <  2:324650/149‑1 (MQ=255)
                                                   cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                   <  1:382176/149‑1 (MQ=255)
                                                     agaagGAGACAACTGACTGATATTCAGAGATTTCTGCGAGCAATATGTTTTCCTTTATTTTCCCAGAAAGCTGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                 <  1:1144259/149‑1 (MQ=255)
                                                       aagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc                                                                               >  1:732005/1‑149 (MQ=255)
                                                       aagTAGACAACTGACTGATAGCAAGAGATTTCTTCGAGCATCGCGTGTGCCTTTATTTTCGATCACATCCGGAGTGTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc                                                                               >  2:1387881/1‑149 (MQ=255)
                                                        agTAGACAACTGACTGATATCCAGAGAATTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca                                                                              <  2:955505/149‑1 (MQ=255)
                                                            gACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcacaca                                                                          >  2:107684/1‑149 (MQ=255)
                                                              cAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATGTTTCAGTGCCATATTGTTCCTCACAGGGAGACAtt                                                                        >  1:164198/1‑149 (MQ=255)
                                                                 ctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTCTTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGt                                                                     <  1:1138647/149‑1 (MQ=255)
                                                                            ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                          >  2:1178048/1‑149 (MQ=255)
                                                                              agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTTCCGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa                                                        >  1:398916/1‑149 (MQ=255)
                                                                              agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTTGTAATGAAAAAAAGa                                                        >  1:881940/1‑149 (MQ=255)
                                                                                  aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaa                                                    <  1:168131/149‑1 (MQ=255)
                                                                                     tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCATTGCCATATTGTTACTCCCATGCACACATTGGTAATTAAACAAAGACAAAaca                                                 >  2:411601/1‑149 (MQ=255)
                                                                                     tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAACAGAGACAAAaca                                                 >  2:947433/1‑149 (MQ=255)
                                                                                       ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑AAGAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg                                               >  1:1255613/1‑149 (MQ=255)
                                                                                           atcAATATGTTTTCCTTTCTTTTCCCAGAAGGCCGGATTTTTTGGTTGCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTCCTCATTTTGCAGTGCCATATTGTTCTTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGt                                           <  2:219365/147‑1 (MQ=255)
                                                                                              aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                        <  1:1313073/149‑1 (MQ=255)
                                                                                                  tGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcgc                                    <  1:806339/149‑1 (MQ=255)
                                                                                                     tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt                                 >  2:82667/1‑149 (MQ=255)
                                                                                                        ccTTTATTTTCCCAGAAGCCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc                              <  1:634590/149‑1 (MQ=255)
                                                                                                          tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACCTGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                            >  1:997405/1‑149 (MQ=255)
                                                                                                             aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtt                         <  1:1178048/149‑1 (MQ=255)
                                                                                                                          gCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAg                                             >  1:198063/1‑116 (MQ=255)
                                                                                                                          gCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAg                                             <  2:198063/116‑1 (MQ=255)
                                                                                                                              gATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCTGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCACAATAGCCAGTCATTCAAATTAAgattac        >  2:1441281/1‑144 (MQ=255)
                                                                                                                                   tCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg   <  1:1387881/149‑1 (MQ=255)
                                                                                                                                   tCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGAAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg   <  1:356209/149‑1 (MQ=255)
                                                                                                                                   tCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg   <  1:350709/149‑1 (MQ=255)
                                                                                                                                    cTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg  <  2:881940/149‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                      
TTTTATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGG  >  NC_000913_3_pae_tpiA/1543874‑1544153

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑