Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273262,0690TG54.5% 4.9 / 10.6 11T66P (ACC→CCC) BW25113_RS25425hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTG  >  NZ_CP009273/261984‑262149
                                                                                     |                                                                                
gTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGa                                                                              <  2:59624/90‑1 (MQ=255)
  tttttCCTGCGTATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGAcc                                                                            <  1:9239/90‑1 (MQ=255)
                        tagtagtaACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAGGGGGGGGCGGGGAAATAGTCAACCCGTGAc                                                      >  2:288294/1‑90 (MQ=21)
                               aaCTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAGGGGGGGCCGGGTAAGTAGGCAACCTGTGACCAttctt                                               >  2:50/1‑90 (MQ=21)
                                 cTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAGGGGGGGCCGGGTAAAAAGGCAACCCGTGGCCAttctttc                                             >  2:311628/1‑88 (MQ=16)
                                   gCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCt                                           <  1:288294/90‑1 (MQ=255)
                                   gCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAAATGCCAAGGGGGGCCGGGTAAAGAATCAACCTGGGAGCCgtcttcccc                                           >  1:145303/1‑87 (MQ=255)
                                    ccATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAGGGGGGGCCGGGTAAAAAGTCAAACCGTGACCATTCTTCCCTg                                          >  2:294893/1‑90 (MQ=21)
                                                   tCGGGCGACTGGCGGGGACGTAAAACCTGCAAAGGGGGACCGGATAAAAAGTCAAACCGTGACCCCTTTTCCCTGACACCATCCtggtgg                           >  2:295018/1‑90 (MQ=255)
                                                         gACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGAcc                     <  2:50034/90‑1 (MQ=255)
                                                                            ccTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTg  <  1:50574/90‑1 (MQ=255)
                                                                                     |                                                                                
GTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTG  >  NZ_CP009273/261984‑262149

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑