Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,267,2780TG57.1% 8.6 / 14.0 14T10P (ACC→CCC) chaAsodium‑potassium/proton antiporter ChaA
Reads supporting (aligned to +/- strand):  ref base T (1/5);  new base G (8/0);  total (9/5)
Fisher's exact test for biased strand distribution p-value = 3.00e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTA‑TGGTTATCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAAT  >  NZ_CP009273/1267199‑1267350
                                                                                |                                                                          
aGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGcc                                                                  <  2:187030/90‑1 (MQ=255)
 gtgtCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTCccccc                                                                 >  2:355790/1‑89 (MQ=255)
     cTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTTCCCCTCttt                                                             >  1:480985/1‑89 (MQ=255)
                   acaGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTa                                              <  1:153921/90‑1 (MQ=255)
                          cAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTA‑TGGTTAt                                      <  2:160885/90‑1 (MQ=255)
                          aggCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTA‑TGGTTAt                                      <  1:552419/88‑1 (MQ=255)
                                 aCCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTTCCCCCCTTTTGCATTTTTCA‑TTATTGTTTTTCCCttt                                >  1:740452/1‑90 (MQ=255)
                                    aGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCCCCCCCTT‑AGCATTTTACA‑TTT‑TTGTTTTTCCTTTTCAg                            >  2:135336/1‑90 (MQ=255)
                                    aGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTTCCCCCCTTTAGCATTTTTCATTTT‑TGGTTTTCCttttctg                             >  2:30709/1‑87 (MQ=255)
                                      cgcCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTTCCCCTCTTGGGCATTTTACA‑TTT‑TTGTTTTCCCCTTGCACAt                          >  1:726369/1‑90 (MQ=255)
                                                gggAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTCCGCCCCTTGAGCATTTTACA‑TTA‑TGGTTTTTCCTTTTCAGAAGGATTTAttg                >  1:116910/1‑88 (MQ=255)
                                                gggAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTCCCCCTCTTGTGCATTTGACA‑TTT‑TGGTTTTTCCTTTGCAGATGAAttttttg                >  1:265420/1‑86 (MQ=255)
                                                gggAAAATAAGCGAAGTCTCCTTGTGGC‑GGGGTTTTTCCCCCCCTTTTGCAATTTAAA‑TTT‑TTGTTTTTCCTTTTCGGATGGAATTAttg                >  2:510631/1‑88 (MQ=255)
                                                              aGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTA‑TGGTTATCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAAt  <  2:740452/90‑1 (MQ=255)
                                                                                |                                                                          
AGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGC‑GGGTTTTTACCGCCTCTTGAGCATTTGACA‑TTA‑TGGTTATCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAAT  >  NZ_CP009273/1267199‑1267350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑