Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273262,0600CA63.6% ‑2.3 / 12.7 11V69F (GTT→TTT) BW25113_RS25425hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (7/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 3.03e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.15e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGG  >  NZ_CP009273/261973‑262124
                                                                                       |                                                                
gTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGGCGTAAAAACt                                                                >  2:292709/1‑90 (MQ=25)
     tGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAGGTAAAAACTGCAAg                                                           >  1:45617/1‑90 (MQ=25)
                   cTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATaa                                             <  2:202428/90‑1 (MQ=255)
                     gCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAagt                                           <  2:63617/90‑1 (MQ=255)
                               gAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGGCGGAAAAACTGCCAAGGGGGGCCGGGTAAGAAGGCaaaccg                                 >  1:87911/1‑86 (MQ=16)
                                     gtagtaACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAAGGGGGGCCCGGTAAGGAGTCAACCTGTGAccc                           >  2:254651/1‑89 (MQ=21)
                                          aaCTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAGGGGGGGCCGGGGAAGGAGTCAACCCGTGGCCcttctt                      >  1:2750/1‑90 (MQ=255)
                                            cTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAAGGGGGACCGGGTAAATAGTCAAACTGTGACCCttcttcc                    >  2:337974/1‑89 (MQ=25)
                                              gCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCt                  <  2:441104/90‑1 (MQ=255)
                                               ccATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTg                 <  2:2750/90‑1 (MQ=255)
                                                              tCGGGCGACTGGCGGGGACGTAAAAACTGCAAAGGGGGGCCGGATAAGTAGTCAACCTGTGACCATTCTTTGCTGACATCATCCctgtgg  >  2:505652/1‑90 (MQ=18)
                                                                                       |                                                                
GTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGG  >  NZ_CP009273/261973‑262124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑