Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,215,3930AG51.7% 32.0 / 39.5 29D190G (GAT→GGT) ebgRtranscriptional regulator EbgR
Reads supporting (aligned to +/- strand):  ref base A (5/9);  new base G (15/0);  total (20/9)
Fisher's exact test for biased strand distribution p-value = 2.00e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.77e-06
Rejected as consensus: Frequency below/above cutoff threshold.

GAAATCATCGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCGCGGCGGTTTTTCCAGTTCG  >  NZ_CP009273/3215314‑3215481
                                                                               |                                                                                        
gAAATCATCGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGGGGAGATGAGCCCGGGAAGGAGGATATTTGTGAg                                                                                >  1:296256/1‑90 (MQ=255)
gAAATCATCGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGGGGAGAAGAGCCTGGGAAGGCGGGTATTtgtggg                                                                                >  2:407599/1‑88 (MQ=255)
  aaTCATCGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATTAGGCCGGGAAGGGGGGAATTTGTGATGt                                                                              >  2:486930/1‑90 (MQ=255)
   atcatcGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGGGAAGAAGAGCCCGGCAAAGCGGGGATTTGTGGGGTc                                                                             >  2:359043/1‑90 (MQ=255)
        cGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCtt                                                                        <  2:359395/90‑1 (MQ=255)
           cTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGc                                                                     <  1:403794/90‑1 (MQ=255)
           cTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGc                                                                     <  1:579115/90‑1 (MQ=255)
             tCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGGGGGTATTTGTGGGGGCGCCttttggg                                                                   >  1:484465/1‑86 (MQ=255)
                    cAACCAGGGCGTTAATCGAATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGGGGGTATTTGTGGGGTCGCCTTTTCGGGATATgg                                                            >  2:78624/1‑90 (MQ=255)
                     aaCCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGGAAATGAGCCCGGCAAGGCGGGTATTTTTGGGGGCGCCCTTTCGGGATATggg                                                           >  2:579115/1‑89 (MQ=255)
                     aaCCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGGGGGTATTTGTGGGGGCGCCCTTTCGGGAAATGGc                                                           >  2:81352/1‑90 (MQ=255)
                     aaCCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGGTATTCGTGAGGGCGCCTTTGCGGGATATGGc                                                           >  1:22234/1‑90 (MQ=255)
                     aaCCAGGGCGTTAATCGTATTGGTTTTATTGGCGGGGAAGATGAGCCTGGCAAGGCGGGTATTTGGGAGGGCGCCTTTTGGGGATATGGc                                                           >  1:355900/1‑90 (MQ=255)
                       ccAGGGCGTTAATCGTATTGGTTTTATTGGCGGGGGAGATTAGGCCGGCAAAGGGGGGATTTGTGAGGGCGCCTTTGCGGAATATGGCCg                                                         >  2:430496/1‑90 (MQ=255)
                         aGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGAc                                                       <  2:321215/90‑1 (MQ=255)
                          gggCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGGTATTCGTGAGGGCGCCCTTTCGGGATATGGCCGGCt                                                      >  2:236838/1‑90 (MQ=255)
                          gggCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCCGGCAAGGCGGGTATTTGTGGGGTGGCCTTTGCGGAAAATGGGCGGCt                                                      >  2:406595/1‑90 (MQ=255)
                            gCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGGTATTCGTGAGGGCGCCTTTGCGGGATATGGCCGACTGa                                                    >  1:243002/1‑90 (MQ=255)
                                 aaTCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGGGGGTATTTGTGAGGGCGCCTTTTCGGGATATGGGCGACTGAAACaa                                               >  2:126497/1‑90 (MQ=255)
                                    cGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGGGGGTATTTGTGGGGGGGCCCTTTCGGGAAATTGGCGACTGaaaaaaaag                                            >  2:425479/1‑87 (MQ=255)
                                       aTTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTa                                         <  1:305290/90‑1 (MQ=255)
                                            ttttATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGa                                    <  1:406595/90‑1 (MQ=255)
                                             tttATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGaa                                   <  1:81352/90‑1 (MQ=255)
                                                              tGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCgcgg                  <  1:126497/90‑1 (MQ=255)
                                                                 gCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCgcgg                  <  2:331782/87‑1 (MQ=255)
                                                                 gCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCgcgg                  >  1:331782/1‑87 (MQ=255)
                                                                   cTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCGCGGCGGtt             >  1:10989/1‑90 (MQ=255)
                                                                          ggCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGATGATATCTGGCGCGGCGGTTTTTCCAg      >  2:13422/1‑90 (MQ=255)
                                                                              gATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCGCGGCGGGTTTTCCAGTtcg  >  2:125153/1‑90 (MQ=255)
                                                                               |                                                                                        
GAAATCATCGACTTCTATATCAACCAGGGCGTTAATCGTATTGGTTTTATTGGCGGTGAAGATGAGCCTGGCAAGGCGGATATTCGTGAGGTCGCCTTTGCGGAATATGGCCGACTGAAACAAGTGGTACGCGAAGAGGATATCTGGCGCGGCGGTTTTTCCAGTTCG  >  NZ_CP009273/3215314‑3215481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑