Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273341,0390CA48.0% 30.8 / 17.4 25intergenic (+337/‑76)BW25113_RS01680/BW25113_RS01685hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (13/0);  new base A (0/12);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 1.92e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCA  >  NZ_CP009273/340977‑341125
                                                              |                                                                                      
ttttttttttATCTTCCCCACCCCCCACAAGCCAAAAAAAAAATATGCTGAAAGCCTCAAATAAAAAACCGCCATTAGCTCATCAGGAag                                                             <  2:319477/88‑1 (MQ=255)
ttttttCTTTATCTACCCCACCCCCCCCAACCCTAAAAAAAAATATGCTGAAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAag                                                             <  1:318180/88‑1 (MQ=255)
     tCTGTATCTTACGCATCGCCCTCAAGCCTGACAAAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAg                                                        <  2:141420/90‑1 (MQ=255)
             ttACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAAc                                                >  1:85393/1‑90 (MQ=255)
              tccGCACCCCACCCAAGCCGGAAAAAAAATATGCTGTAAGGCTCATACAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAAcc                                               <  2:226758/88‑1 (MQ=255)
              tACGCACCGCACTCAAGCCTAAAAAAAAATATGCTGAAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAAcc                                               <  1:74063/90‑1 (MQ=255)
              tACGCACCCCCCCCAGGCCTAAAAAAAAATTTGCTGAAGGCCTCATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAAcc                                               <  1:31349/90‑1 (MQ=255)
              tACGCACCCCCCCCAAGCCTAAAAAAAAATATGCTGTAAGGCTAATAAAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAAcc                                               <  1:158776/90‑1 (MQ=255)
                  cATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGa                                           >  2:185444/1‑90 (MQ=255)
                   aTCGCACTCAAGCCTGAAAAAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt                                          <  2:126948/90‑1 (MQ=255)
                   aTCGCACCCAAGCCTAAAAAAAAATATGTTGTAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt                                          <  2:391763/90‑1 (MQ=255)
                   aTCCCACACAAGCCTGAAAAAAAATATGCTGAAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt                                          <  1:414067/90‑1 (MQ=255)
                    tCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAtt                                         >  1:126948/1‑90 (MQ=255)
                    tCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAtt                                         >  1:213524/1‑90 (MQ=255)
                      gCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgt                                       >  2:42595/1‑90 (MQ=255)
                      gCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgt                                       >  2:368857/1‑90 (MQ=255)
                                cTGAAAAAAAATATGCTGAAAGGCTCATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTAc                             <  2:341886/90‑1 (MQ=255)
                                          atatGCTGTAAGGCTCATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAg                   <  2:268518/90‑1 (MQ=255)
                                                tGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCg             >  2:310149/1‑90 (MQ=255)
                                                tGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCg             >  1:66961/1‑90 (MQ=255)
                                                 gTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTTTATGGTACGGGGTTCGAGGCCTCGa            >  2:130514/1‑90 (MQ=255)
                                                      gCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCg       >  1:129949/1‑90 (MQ=255)
                                                         cATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTc    >  1:54425/1‑90 (MQ=255)
                                                         cATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTc    >  1:151819/1‑90 (MQ=255)
                                                           tatCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCa  >  2:322258/1‑90 (MQ=255)
                                                              |                                                                                      
TCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCA  >  NZ_CP009273/340977‑341125

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑