Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,570,3260TC54.5% 4.2 / 10.1 11G517G (GGA→GGG) yddBTonB‑dependent receptor plug domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAA  >  NZ_CP009273/1570242‑1570399
                                                                                    |                                                                         
ataAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCat                                                                      >  2:276758/1‑90 (MQ=255)
     gCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCaa                                                                 >  1:207306/1‑90 (MQ=255)
        ttttCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGaa                                                              <  2:269437/90‑1 (MQ=255)
                    gATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGAAATCCCATATCAAGAATATTCCCGCCAt                                                  >  2:405409/1‑90 (MQ=255)
                          gcgTTAGATTTTTATTCCCTGATCCCGATCCCGCCCAGCTATTGCGGATATCACGTAACCCCATATAAAAAATATTCCCGCCATAGTAAc                                            <  1:26004/90‑1 (MQ=255)
                          gcgTCAGATTTTTTTTCCCTGATCCCGTTCCCGCCCAGCTTTTGCGGATATCACGTAACCCCATATAAAGAATATTCCCGCCATAGTAAc                                            <  1:9749/90‑1 (MQ=255)
                                    tttATTCCCTAATACCTTTCCCCCCCAGTTTTGGGGAATATCACAAAACCCCATAAAAAAAATTTTCCCGCCATAGTAACGGTTATAAcc                                  <  2:94577/90‑1 (MQ=255)
                                    tttATTACCTGATCCCGTTCCCGCCCAGTTATTGGGGATATCACGTAACCCCATATAAAAAATATTCCCGCCATAGTAACGGTTATAAcc                                  <  1:155069/90‑1 (MQ=255)
                                         tcccTGTTCCCGTTCCCCTCCAGTTTTTGGGGATATCAGGTAACCCAATAAAAAAATTTTCCCCGCCATAGTAACGGTTATAACctgctg                             <  2:89033/88‑1 (MQ=255)
                                                          gTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGa            >  1:273317/1‑90 (MQ=255)
                                                                    tGCGGATATCACGTAACCCCAAAAAAAAAATTTCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCaaaaa  <  1:319563/90‑1 (MQ=255)
                                                                                    |                                                                         
ATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAA  >  NZ_CP009273/1570242‑1570399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑