Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,033,5620TA58.3% 2.2 / 11.0 12Y202N (TAT→AAT) msrPprotein‑methionine‑sulfoxide reductase catalytic subunit MsrP
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base A (7/0);  total (8/4)
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.

CTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACC  >  NZ_CP009273/2033491‑2033647
                                                                       |                                                                                     
cTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGGAAAAAACTTTTTTCGAAGGag                                                                     >  2:221289/1‑89 (MQ=255)
 tttCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGAtt                                                                    <  2:122515/90‑1 (MQ=255)
  ttCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTTTTTCGAAGGAATg                                                                   >  1:179204/1‑90 (MQ=255)
  ttCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGGGGAAAATACTTATTTCGAAGGATTg                                                                   >  2:310890/1‑90 (MQ=255)
                acagccGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGc                                                     <  1:59144/86‑1 (MQ=255)
                              tGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGGGGAAAATACCTTTTTTGAAGGAATGGGTCTCGGCGAAACAAAACAACCGCtgt                                       >  2:59144/1‑88 (MQ=255)
                              tGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAAAATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTca                                       >  1:206630/1‑90 (MQ=255)
                                   ggccagCAGGACCGCTTTATCGGCGGGGGGGTGGAAAATCCTTTTTTTGAAGGATTGGGTCTCGACGAAGCAAAGCATCCGCCCCCACtg                                  >  2:187553/1‑90 (MQ=255)
                                             aCCGCTTTATCGGCGGGGGGGTGAAAAATTCTTATTTCGAAGGATTTCGTCTCGACGAAACAAAGCATCCCCCCACACTGATGACCCTAg                        >  1:433442/1‑90 (MQ=255)
                                              ccGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAgg                       <  1:554247/90‑1 (MQ=255)
                                                                   gAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTAcc  >  1:124784/1‑90 (MQ=255)
                                                                   gAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTAcc  <  1:33684/90‑1 (MQ=255)
                                                                       |                                                                                     
CTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTCGAAGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACC  >  NZ_CP009273/2033491‑2033647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑