Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,251,3610AC74.2% 55.9 / 21.9 31C162W (TGT→TGG) psuGpseudouridine‑5'‑phosphate glycosidase
Reads supporting (aligned to +/- strand):  ref base A (4/4);  new base C (10/13);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.14e-02
Rejected as consensus: Frequency below/above cutoff threshold.

AATGCTGACGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCGGCAAG  >  NZ_CP009273/2251226‑2251483
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aaTGCTGACGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGACGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGcaca                                                                                                                          >  2:171191/1‑138 (MQ=255)
        cGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGt                                                                                                                 <  2:281369/139‑1 (MQ=255)
        cGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGt                                                                                                                 <  1:837341/139‑1 (MQ=255)
        cGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGt                                                                                                                 <  1:560005/139‑1 (MQ=255)
            aaaCGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACa                                                                                                             >  1:349470/1‑139 (MQ=255)
                  gCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTa                                                                                                       <  2:556243/139‑1 (MQ=255)
                             cagaaaaCGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTc                                                                                            >  2:301929/4‑139 (MQ=255)
                                            gcgcTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGa                                                                             <  2:750511/139‑1 (MQ=255)
                                                     tCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCg                                                                      >  1:52608/1‑137 (MQ=255)
                                                     tCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCg                                                                      <  2:52608/137‑1 (MQ=255)
                                                         aTAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAg                                                                   <  2:65910/136‑1 (MQ=255)
                                                                   aaCGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGcc                                                       <  2:811837/138‑1 (MQ=255)
                                                                       gCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCcgc                                                   >  2:371449/1‑138 (MQ=255)
                                                                               aaGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCacac                                          <  1:362064/139‑1 (MQ=255)
                                                                                             cTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCg                            <  1:371449/139‑1 (MQ=255)
                                                                                               cAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGt                          >  2:168011/1‑139 (MQ=255)
                                                                                                aGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCAcacc                                         <  1:623336/123‑1 (MQ=255)
                                                                                                aGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCAcacc                                         >  2:623336/1‑123 (MQ=255)
                                                                                                aGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACAt                                                                                                            <  1:544708/56‑1 (MQ=255)
                                                                                                aGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACAt                                                                                                            >  2:544708/1‑56 (MQ=255)
                                                                                                 gTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTgg                        >  1:775989/1‑139 (MQ=255)
                                                                                                     ttAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGca                                             >  2:350567/1‑114 (MQ=255)
                                                                                                     ttAATCCTAAATCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGca                                             <  1:350567/114‑1 (MQ=255)
                                                                                                               aTCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCcgcg                                                  <  1:640375/99‑1 (MQ=255)
                                                                                                               aTCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCcgcg                                                  >  2:640375/1‑99 (MQ=255)
                                                                                                               aTCGAGAATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAAtt          <  2:522220/139‑1 (MQ=255)
                                                                                                                   agaATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCgg      >  1:713322/1‑139 (MQ=255)
                                                                                                                   agaATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCgg      >  2:730332/1‑139 (MQ=255)
                                                                                                                    gaATAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCgg      >  2:308464/1‑138 (MQ=255)
                                                                                                                       tAGATTTCGCCCCGGCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCGGCAAg  <  1:730332/139‑1 (MQ=255)
                                                                                                                                    ggCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGcc                                                       >  2:290692/1‑73 (MQ=255)
                                                                                                                                    ggCCCAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGcc                                                       <  1:290692/73‑1 (MQ=255)
                                                                                                                                       |                                                                                                                          
AATGCTGACGTCAAACGGGCTGGTGCGGCAGAAAAACGCAGGCAGCGCTTTAGTCTGATAGCCAATTAACGGCACACCGAAGGTTTCTAAATACTCAGTGGTTAATCCTAAATCGAGAATAGATTTCGCCCCGGCACAAACAACGGTGACATTAGTATTTGCCAGTTCTTGCAAATCGGCAGAAATATCGAAGGTATGTTCCGCCCCGCGATGCACACCACCAATTCCCCCGGTGGCAAATACTTTAATTCCGGCAAG  >  NZ_CP009273/2251226‑2251483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑