Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,475,2830GA58.3% 3.5 / 11.9 12P125S (CCA→TCA) emrYmultidrug efflux MFS transporter permease subunit EmrY
Reads supporting (aligned to +/- strand):  ref base G (4/1);  new base A (0/7);  total (4/8)
Fisher's exact test for biased strand distribution p-value = 1.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAA‑CTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAT  >  NZ_CP009273/2475215‑2475361
                                                                     |                                                                              
ccATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAA‑CTCTGTGACAGTGGAATTAACGGCCCCGCCATTaa                                                           >  1:215794/1‑90 (MQ=255)
  aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAA‑CTCTGTGACAGTGGAATTAACGGCCCCGCCATTAAcc                                                         >  1:566832/1‑90 (MQ=255)
                    tttttttttCGGGGGAATAATTCTTAAAAAAAAAA‑CTCTGGGAAAGTGAAATTACCGGCCCCGCCATTAACCCCTGAACGACTCTaaaaa                                       <  1:119437/87‑1 (MQ=255)
                            tcgggCGAATATTTCTTAAAAAAAAAA‑CTCTGTAAAAGTGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGc                               <  2:524420/87‑1 (MQ=255)
                                         tCCTTAAAAAAAAACCTCTGGGAAAGTGAATTAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTg                   <  1:188639/90‑1 (MQ=255)
                                              aaaaataaA‑CTCTGTAAAAGTAAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGAt             <  2:388987/87‑1 (MQ=255)
                                                     aa‑CTCTGTGACAGTAAAATAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTac      <  1:271675/90‑1 (MQ=255)
                                                      acctctGTGAAAGGGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTac      <  1:93425/88‑1 (MQ=255)
                                                          ttgtgACAGTGAAATTACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAt  <  1:484018/89‑1 (MQ=255)
                                                          ctGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAt  >  2:239609/1‑90 (MQ=255)
                                                                 aGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATa            <  1:193482/73‑1 (MQ=255)
                                                                 aGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATa            >  2:193482/1‑73 (MQ=255)
                                                                     |                                                                              
CCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAA‑CTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAT  >  NZ_CP009273/2475215‑2475361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑