Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,142,2370TG54.2% 14.6 / 27.2 24T264P (ACC→CCC) ppcphosphoenolpyruvate carboxylase
Reads supporting (aligned to +/- strand):  ref base T (1/10);  new base G (13/0);  total (14/10)
Fisher's exact test for biased strand distribution p-value = 5.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.28e-05
Rejected as consensus: Frequency below/above cutoff threshold.

GTTCAGAAACCAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCGACGGGCAG  >  NZ_CP009273/4142159‑4142321
                                                                              |                                                                                     
gTTCAGAAACCAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGAAATTggggg                                                                            >  2:193399/1‑87 (MQ=255)
          cAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGt                                                                           <  1:577935/81‑1 (MQ=255)
          cAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGt                                                                           >  2:577935/1‑81 (MQ=255)
          cAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGTGACGTTTgg                                                                 >  1:577527/1‑90 (MQ=255)
                     tatCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTcgc                                                      <  2:721145/90‑1 (MQ=255)
                         tttCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGGGACGTTTGGGGTGGCGCCGCgggc                                                  >  2:37224/1‑88 (MQ=255)
                            cAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATTGGCAGGGGCGTTTGGGGTTCCCTCGCGGGcgcc                                               >  2:662771/1‑90 (MQ=255)
                            cAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGGGAACGTCCGGGTGCCggcgccggcgcc                                               >  2:324530/1‑90 (MQ=255)
                            cAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGGGAAGTTTGGGGTGCCGTCGCGGGcgcc                                               >  1:494786/1‑90 (MQ=255)
                                 aCAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGTGACGTTCGGGGTGCCGTCGCGGGCGccccccc                                          >  1:331986/1‑89 (MQ=255)
                                      tCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCAc                                     <  1:570127/90‑1 (MQ=255)
                                      tCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCAc                                     <  2:577527/90‑1 (MQ=255)
                                      tCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCAc                                     <  1:266204/90‑1 (MQ=255)
                                           ggCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGt                                <  2:54016/90‑1 (MQ=255)
                                              tttCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGTGACGGTCGGGGTGCCGTCGCGGGCGCCGCCCCTCCCCGAAGTaaa                             >  1:334577/1‑90 (MQ=255)
                                              tttCCAGCGGCTGAGTAGCAGGACGTGGCGGGGGATATCGGCAGGGGCGTTCGGGGTGCCGGCGCGGGCGCCGCCCCTCCACCAAGGaaa                             >  2:266204/1‑90 (MQ=255)
                                                      ggCTGAGTAGCAGGACGTGGCGGGGGGTATCGGCAGTGTCGTTCGGGGTGGCGGCGGGGGGGGCGCCCGGCCCCGAGGGAAAAAGGGCCg                     >  2:455380/1‑90 (MQ=255)
                                                                 aGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGGCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCg          >  1:191362/1‑90 (MQ=255)
                                                                    aCGTGGCGGGGGATATCGGCAGTGACGTTCGGGGTGCCGTCGCGGGCGCCGCCCCTCCCCGAAGGAAAAAGGACCGGAACAAATTctgtc       >  2:383307/1‑86 (MQ=255)
                                                                       tGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCGACGGGc    <  1:58395/90‑1 (MQ=255)
                                                                       tGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCGACGGGc    <  1:707716/90‑1 (MQ=255)
                                                                         gCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCGACGGGCAg  <  1:324530/90‑1 (MQ=255)
                                                                         gCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGCCGCGGTCGCCGCCCATCCACGAAATAAAACGGACCGGAACAAATTCGACGGGCAg  <  1:37224/90‑1 (MQ=255)
                                                                         gCGGGGGATATCGGCAGTGACGTTCGGGGTGCCGGCGCGGGCGCCCCCCCTCCCCGGAGGAAAAAGGGCCCGGAAAAATTCGACggggcg  >  2:440605/1‑87 (MQ=255)
                                                                              |                                                                                     
GTTCAGAAACCAGCACCTGAATATCTTTCAGGAACAAATCGGTGGCTTTCCAGCGGCTGAGTAGCAGGACGTGGCGGGTGATATCGGCAGTGACGTTCGGGTTGCCGTCGCGGTCGCCGCCCATCCACGAAGTAAAACGGACCGGAACAAATTCGACGGGCAG  >  NZ_CP009273/4142159‑4142321

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: