Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273842,9010AT54.5% 6.0 / 12.8 11I187N (ATC→AAC) glnHglutamine ABC transporter substrate‑binding protein GlnH
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base T (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTTTCGGGAACGCAATACCGTATTGCTGCGCTTCCAGAGAGTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTGGTGCCCAGTTCCATATAGG  >  NZ_CP009273/842821‑842970
                                                                                |                                                                     
cTTTCGGGAACGCAATACCGTATTGCTGCGCTTCCAGAGAGTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACa                                                              <  2:299497/90‑1 (MQ=255)
              aTACCGTATTGCTGCGCTTCCAGAGAGTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTtga                                                                       <  2:145657/67‑1 (MQ=255)
                           gcgcTTCCAGAGAGTCACCTACCGCTTTGAACTGACCGTTACCGGCGGGTTTTTTGAAGGAAAGAAAGTTTTGGGGATCGTGCAGAACgg                                   >  2:367684/1‑90 (MQ=255)
                                        gTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTTTTGAAGGACAGAATGTTTTGCGGATCGTGCAGAAAGGCGGCTGCGCgggt                      >  1:89370/1‑88 (MQ=255)
                                        gTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTGTTGAAGTACAGAAAGTTTGGGGGATCGTGCAGAACGGGGGCTGCGCgggt                      >  2:14534/1‑88 (MQ=255)
                                          cACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTgg                    <  2:50247/90‑1 (MQ=255)
                                               aCCGCTTTGAGCTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTGGTGccc               <  1:32535/90‑1 (MQ=255)
                                               aCCGCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTGGTGccc               <  1:291216/90‑1 (MQ=255)
                                                  gCTTTGAACTGACCGTTACCGGCGGTTTTTTTGAAGTACAGAATGTTTGGCGGATCGTGCAGAAAGGCGGCTGCGCGGGTGGTGGCCAGt            >  1:194760/1‑90 (MQ=255)
                                                  gCTTTGAACTGACCGTTACCGGCGGTTTTTTTGAAAGACAGAAAGTTTTGGGGATCGTGCAGAACGGGGGCTGCGCGGGTTGGGCCCCGt            >  2:32535/1‑90 (MQ=255)
                                                  gCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTGGTGCCCAGt            <  1:56361/90‑1 (MQ=255)
                                                            gACCGTTACCGGCGGGTTTGTTGAAGTACAGAAAGTTTTGGGGATCGTGCAGAACGGGGGCTGCGCGGGTGGGGGCCAGTTTCCtataag  >  2:190850/1‑88 (MQ=255)
                                                                                |                                                                     
CTTTCGGGAACGCAATACCGTATTGCTGCGCTTCCAGAGAGTCACCTACCGCTTTGAACTGACCGTTACCGGCGGTTTTGATGAAGTACAGAATGTTTGGCGTATCGTGCAGAACGGCGTCTGCGCGGTTGGTGCCCAGTTCCATATAGG  >  NZ_CP009273/842821‑842970

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: ‑