Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,778,6860TG58.3% 5.2 / 11.0 12intergenic (‑316/+435)BW25113_RS25705/BW25113_RS13825DUF5507 domain‑containing protein/tRNA‑Ile
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (7/0);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTCAATAGCGTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCATTGTTCTACATACATTGGTTGTGGTAC  >  NZ_CP009273/2778615‑2778774
                                                                       |                                                                                        
ctcAATAGCGTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGa                                                                        <  2:243451/90‑1 (MQ=255)
  cAATAGCGTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGGGGTTTTGTTAGTAGgagaag                                                                      >  1:349869/1‑88 (MQ=255)
         gTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGTGTTc                                                                                      <  2:104257/67‑1 (MQ=255)
         gTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGGGTTc                                                                                      >  1:104257/1‑67 (MQ=255)
                     gCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGGGTTTTGGGCAGGAGTAGATGTTTTAGGGGGGGGagaggc                                                   >  2:99873/1‑88 (MQ=255)
                             aCGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGGGGTCTGGGCCGTAGTAGGTGTTTAAAGGGGGGGCGAGACAATTTATc                                           >  2:78606/1‑90 (MQ=255)
                                          gCTCACAAAACTCATCTGCCTGCGGCGGGGGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACAATTTATCCTTTCTCTACGGc                              >  2:150184/1‑90 (MQ=255)
                                          gCTCACAAAACTCATCTGCCTGCGGCGGGGGTTCTGGTCAGGAGGAGATGTTTAAGGCGGGGGGGAGACAATTTATCCTTACCCTACGGc                              >  2:71683/1‑90 (MQ=255)
                                            tCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCAt                            <  1:150184/90‑1 (MQ=255)
                                            tCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCAt                            <  1:75346/90‑1 (MQ=255)
                                            tCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCAt                            <  1:78606/90‑1 (MQ=255)
                                                           gcctgcGGCGGGGGTTCTGGTCAGTAGTAGATGTTTAAAGCGTGGCCGAGGCATTTTATCCTTTCTCTACGGCAATGTTTTACATACAtt             >  2:274539/1‑90 (MQ=255)
                                                                      gtgtTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCATTGTTCTACATACATTGGTTGTGGTAc  <  2:349869/90‑1 (MQ=255)
                                                                       |                                                                                        
CTCAATAGCGTTGGTTAATGAGCATAGCCACGCTCCTGTAACGCTCACAAAACTCATCTGCCTGCGGCGGGTGTTCTGGTCAGTAGTAGATGTTTAAGGCGTGGCAGAGACATTTCATCCTTACTCTACGGCATTGTTCTACATACATTGGTTGTGGTAC  >  NZ_CP009273/2778615‑2778774

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑