Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,033,5620TA53.8% 5.7 / 17.1 13Y202N (TAT→AAT) msrPprotein‑methionine‑sulfoxide reductase catalytic subunit MsrP
Reads supporting (aligned to +/- strand):  ref base T (0/6);  new base A (7/0);  total (7/6)
Fisher's exact test for biased strand distribution p-value = 5.83e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAG  >  NZ_CP009273/2033476‑2033639
                                                                                      |                                                                             
aTGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGAAAAATc                                                                            >  2:81783/1‑90 (MQ=255)
          tGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTTTTTCGa                                                                  >  2:1289515/1‑90 (MQ=255)
                           tttATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTcgacg                                                 <  2:656302/90‑1 (MQ=255)
                            ttATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTcgacga                                                <  2:1606351/90‑1 (MQ=255)
                                  aCCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGAAAAATACTTTTTTTGAAGGATTGGGTCTCCACGAAGGaaa                                          >  1:1340176/1‑89 (MQ=255)
                                   ccGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGAAAAATTCTTTTGTTGGAGGATTGCGTCTCGACGGAGGaaag                                         >  2:506365/1‑88 (MQ=255)
                                         cAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCg                                   <  2:1188095/90‑1 (MQ=255)
                                           gATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGGAAAATCCTTATTTCTAAAAATTTTGTCTCGACGGAGCAAAACATccccg                                 >  2:1264723/1‑87 (MQ=255)
                                                caggccagCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATTCTTTTTTCGGAGGATTTGGTCTCCGCGAAGCAAAGCATCCGCTCacac                            >  2:854483/1‑90 (MQ=255)
                                                caggccagCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCacac                            <  1:854483/90‑1 (MQ=255)
                                                caggccagCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCacac                            <  2:996020/90‑1 (MQ=255)
                                                     cagcagGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACtgatg                       <  2:3844/90‑1 (MQ=255)
                                                                          ggTGGGGTGAAAAATCCTTTTGTCGAAGGATTGCGTCTCGACGAAGCAAAGCATCCGCTCACACTGATGACCCTAGGGGTTTTTGGCAAg  >  2:631462/1‑90 (MQ=255)
                                                                                      |                                                                             
ATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAG  >  NZ_CP009273/2033476‑2033639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑