Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913417,5330TG60.7% ‑5.7 / 15.7 29V131G (GTG→GGG) phoBresponse regulator in two‑component regulatory system with PhoR
Reads supporting (aligned to +/- strand):  ref base T (8/3);  new base G (17/0);  total (26/3)
Fisher's exact test for biased strand distribution p-value = 5.04e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGAGCCGCTGGAGAT‑GGGGCCGAC‑AGAATTTAAACTGCT‑GCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCACGGTCGATGTCCACATTCGTCGCCTGCGTAAAGCACTGGAGCCCG  >  NC_000913/417303‑417766
                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                            
gATGTTACCTGGCGACTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGGCGATTACCCGGGAGATTCCAGGGGTGATGTTGACCGCCAGCGGGGAAGAAGAAGACCGCGTGCGCGGCATTGAAACCGGCGCGGAGGACTATATCACCAAGCCGTTTTCGCAGAAGGTGCTGGTGGTGCGAATGAAAGCGGTAATGCGCCGATTGTCGCCAA‑TGGCGGTGGGAGAGGTGGGTgaga                                                                                                                                                                                                                                      >  2:248979/1‑239 (MQ=255)
  tGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGGGGAAGAGGGGATTGAGATg                                                                                                                                                                                                                                    >  1:1409835/1‑239 (MQ=255)
          ggcggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGGGATGAAGGGAtt                                                                                                                                                                                                                            >  1:844919/1‑239 (MQ=255)
          ggcggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCAAA‑TGGCGGTGGCAGGGGGGATTGAGATGCAGGGGtt                                                                                                                                                                                                                            >  1:1234021/1‑239 (MQ=255)
              gcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGAATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGGGAATCAGGGTTTAAg                                                                                                                                                                                                                         >  1:726637/1‑238 (MQ=255)
                 ccGGTATCCCGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGGGATGTTGACCGCCAGAGGGGAAGAAGAAGAGCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGTGCTGGGGGCGCGAATCAAAGCGGTAATGCGCCGTCTTTCGCCAACGGGCGGTGGACAAGG‑GAATGAGACGTAGGGATTGAGt                                                                                                                                                                                                                        >  2:625842/1‑236 (MQ=255)
                               atcaAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGGGGGGGTTGAGATGCAGGGATTAAGTCTCGACCCGACAtctc                                                                                                                                                                                                        >  1:1254093/1‑238 (MQ=255)
                               atcaAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGGGGGAGAGGGGATTGAGAGGCAGGGATTAAGTGTCGACCCGACAtctc                                                                                                                                                                                                        >  2:336896/1‑238 (MQ=255)
                                           aaGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGAGATGCAGGGGTTAAGGCTCGACCCGACAACTCACCGAgggggggg                                                                                                                                                                                           >  1:1104993/1‑232 (MQ=255)
                                                cgAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGGAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCCACATCTCACCGa                                                                                                                                                                                                   >  1:421104/1‑226 (MQ=255)
                                                  aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGACTCAAAGCGGTAATGCGCCGTATTTCGCCAC‑TGGCGGGGGAAGAGGGGGTTGAGAAGGCGGGATTAAGTCTAGACCCGGCATCTTACCGAGGGATggcggggggg                                                                                                                                                                                    >  2:849657/1‑235 (MQ=255)
                                                  aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGGAGAGGGGATTGAGATGCCGGGATTAAGTCTCGAACCGACATCTCACCGAGGGGTGGCGGGGGaa                                                                                                                                                                                    >  1:1319297/1‑239 (MQ=255)
                                                  aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGGGATGGCGGGCGaa                                                                                                                                                                                    >  1:176892/1‑239 (MQ=255)
                                                  aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTAGCCAA‑TGGCGGGGGGAGAGGGGATTGGGATGCAGGGGTTAAGTCTCGACCCGACATCTCACCGCGTGATgccgggggga                                                                                                                                                                                    >  2:308474/1‑235 (MQ=255)
                                                  aGTCGATGACCCGGGATATTCCAGTGGCGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGGGGGGGTTGGGATGCAGGGGTTTAGGGTCTCCCCGACATCTCCCCGAGGGGTGGGGGGGGag                                                                                                                                                                                    >  2:608892/1‑238 (MQ=255)
                                                                                         ccAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGAAATCTCACCGAGTGATGGCGGGGGCAAAGGCGCCGGGGGT‑GGGGGCGAA‑CGAAATTAAAatgctc                                                                                                                                           >  1:312266/1‑238 (MQ=255)
                                                                                                                                  ggCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGGAGAGGTGATTGAGATGCAGGGATTAAGGCTCGACCCGCCCTCTCACCGAGTGATGGGGGGGGGAGAGCGGCGGGGGGG‑GGGGGCGGC‑AGAACATTAACTGCT‑GCGCCTTTTTTTTTCGCCTCCTCAGCGCCGGTGCAGcccagc                                                                                                 >  2:996620/1‑235 (MQ=255)
                                                                                                                                  ggCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGGGATGGCGGGCGAAGAGCCGCTGgagaa                                                                                                                                                                      >  1:1122123/1‑172 (MQ=255)
                                                                                                                                    cgcgGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGAAAtct                                                                                                                                                                                                         >  1:269158/1‑136 (MQ=255)
                                                                                                                                     gcgcATGACTATCTCACCTAGCCGTTTGCGTCTAAGGAGCTGGTGGCGAGAATCAAAGCGGTAACGCGCCGTATGTCGCCAA‑TGGCGGTGGAAGCGGTGATTGAGATGCAGGGATTAAGTCTCGACGTGACATCGCACCGAGTAACGGCGGGCGATGAGCCGGTGGAGAT‑GGAGCCGAC‑AGAATTTAAACTGGT‑GCTCTTTTTTATGACGCATCCTGGGCTGGTGTAAAGCCGCGagc                                                                                               <  2:1402504/238‑1 (MQ=255)
                                                                                                                                                  tCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGGGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGGGGAGAGACCCCGGGGAT‑GGGGCCGCC‑ACAACTTTAACTGCG‑GCACTTTTTTTTGACACATCCTGTGGGCGGGTTAAGTCGCGCGCCGCCGTTGAAccc                                                                                  >  2:1366291/1‑237 (MQ=255)
                                                                                                                                                        aGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGGAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGGGCAGAGGCGCCGGGGGT‑GGGGGCGGCAAGAATTTAAA‑TGCT‑GCACtttttttttac                                                                                                                            >  2:120576/1‑185 (MQ=255)
                                                                                                                                                        aGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACAtct                                                                                                                                                                                                         >  1:286073/1‑116 (MQ=255)
                                                                                                                                                              tttCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGGGaa                                                                                                                                                                                    >  1:602364/1‑131 (MQ=255)
                                                                                                                                                                                     caattgaaaGCGGTAATGCGCCGTATTCCGCCAA‑TGGCGGTGGAAGAGGTGATTGGGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGAGCCGCTGGAGAT‑GGGGCCGAC‑AGAATTTAAACTGCT‑GCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCa                                               <  2:647800/232‑1 (MQ=255)
                                                                                                                                                                                                  tAATGCGCCGTATTTCGCCAA‑TGGCGGGGGAAGAGGTGATTGAGATGCCGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGGAGAGACGCCGGGGGTGGGGGCCCAC‑A‑AATTTTAACGGGTGGCACTTTTTTTTAGCCCTTCC‑GAGGGCGCGTACAAGCCCGCGCACCTGTTGAACCACGCCTTGGGGACTGACCTGTGTTGGGACAACCCCACgggtgagagctc                                  >  2:1296474/1‑228 (MQ=255)
                                                                                                                                                                                                                                  agagGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGAGGCGCTGGGGAT‑GGGGGCGAC‑AGAATTTAAACTGCT‑GCACCTTTTTATGACGCATCCCTAGCGCGGGTAAAACCGCGAGCAGCTGTTAAACCACGGCTGTGGGACTAACGTGTATGTGGAAGACCCCACGGTCGGTGTCCCAATTCGTCGCCTGCGGGAAGCaacgtgacccg  >  2:914820/1‑229 (MQ=255)
                                                                                                                                                                                                                                   gagGTGATTGAGATGCAGGGAtt                                                                                                                                                                                                                            <  2:504125/23‑1 (MQ=255)
                                                                                                                                                                                                                                      gTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGAGCCGCTGgaga                                                                                                                                                                       >  1:1159778/1‑73 (MQ=255)
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GATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAA‑TGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGAGCCGCTGGAGAT‑GGGGCCGAC‑AGAATTTAAACTGCT‑GCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCACGGTCGATGTCCACATTCGTCGCCTGCGTAAAGCACTGGAGCCCG  >  NC_000913/417303‑417766

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑