Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,764,5940TA29.7% 56.7 / 10.5 38Q187L (CAA→CTA) yfjLCP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
Reads supporting (aligned to +/- strand):  ref base T (17/9);  new base A (10/1);  total (28/10)
Fisher's exact test for biased strand distribution p-value = 2.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AAGGATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCC  >  NC_000913/2764530‑2764660
                                                                |                                                                  
aaGGATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTggg                                                                 >  1:649268/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAg                                                               >  1:112094/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAg                                                               >  2:1474746/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAg                                                               >  2:1000436/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTAGGTAg                                                               >  2:1037544/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTAGGGAg                                                               >  2:929051/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTAGGGAg                                                               >  2:758893/1‑68 (MQ=255)
  ggATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACCGAGAATGACCCCATGTAGATCTAGGGAg                                                               >  2:324142/1‑68 (MQ=255)
    aTGCGGAACCAAATGTCTTCGGCGACGGTTTAGGAACTGAGAATGACACCATGTAGATCTTCGGAGGc                                                             >  1:543956/1‑68 (MQ=255)
       cGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAg                                                          <  1:879356/68‑1 (MQ=255)
        ggCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGc                                                         <  2:312807/68‑1 (MQ=255)
        ggCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGc                                                         <  2:524660/68‑1 (MQ=255)
        ggCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGc                                                         <  1:310129/68‑1 (MQ=255)
           aCCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGt                                                      <  2:764535/68‑1 (MQ=255)
               aaTGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGt                                                  <  1:758897/68‑1 (MQ=255)
               aaTGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGt                                                  <  2:133234/68‑1 (MQ=255)
                                      aaCTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGt                           >  1:634767/1‑68 (MQ=255)
                                      aaCTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGt                           >  1:986675/1‑68 (MQ=255)
                                        cTGAGAATGACCCCATGTAGATCTAGGGAGTCCCCCAGTCTGTTCATAATCACTAGAAGTTCCAGTTc                         >  2:1170733/1‑68 (MQ=255)
                                            gaATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCgcgc                     >  2:470540/1‑68 (MQ=255)
                                               tGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAgg                  <  1:353145/68‑1 (MQ=255)
                                               tGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAgg                  <  1:470543/68‑1 (MQ=255)
                                                 aCCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGCTCCCTAGAAGTTCCAGTTCGCGCAGGGa                >  1:245377/1‑68 (MQ=255)
                                                 aCCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGa                >  1:1468906/1‑68 (MQ=255)
                                                 aCCCCATGTAGATCTAGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGa                >  2:422069/1‑68 (MQ=255)
                                                   cccATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATg              >  2:109885/1‑68 (MQ=255)
                                                   cccATGTAGATCTGGGTAGGCCAGCAGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATg              >  2:1285965/1‑68 (MQ=255)
                                                   cccATGTAGATCTAGGGAGTCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATg              >  2:918793/1‑68 (MQ=255)
                                                   cccATGTAGATCTAGGGAGGCCCGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATg              >  2:1248538/1‑68 (MQ=255)
                                                        gTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAac         >  1:1265130/1‑68 (MQ=255)
                                                         tAGATCTAGGTAGTCCACCAATATGTTATAAATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAacc        >  2:540516/1‑67 (MQ=255)
                                                            aTCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACtt     >  1:679699/1‑68 (MQ=255)
                                                            aTCTTGGGAGGCCAGCCGTATGTTCTTGATCACTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACtt     >  1:1222675/1‑68 (MQ=255)
                                                            aTCTAGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACtt     <  1:1318201/68‑1 (MQ=255)
                                                             tCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTc    >  1:1086265/1‑68 (MQ=255)
                                                             tCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTc    >  1:1087921/1‑68 (MQ=255)
                                                             tCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACATc    >  1:386963/1‑68 (MQ=255)
                                                             tCTAGGTAGTCCACCAGTCTGTTCTTAATACCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTc    >  2:1122519/1‑68 (MQ=255)
                                                               ttGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTccc  <  2:634763/68‑1 (MQ=255)
                                                               ttGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTccc  <  1:1388375/68‑1 (MQ=255)
                                                                |                                                                  
AAGGATGCGGCACCAAATGTCTTCGGCGACGGTTTCGGAACTGAGAATGACCCCATGTAGATCTTGGGAGGCCAGCCGTATGTTCTTGATCCCTAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCC  >  NC_000913/2764530‑2764660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑