Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273341,0130CA55.6% 4.0 / 11.9 9intergenic (+311/‑102)BW25113_RS01680/BW25113_RS01685hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (2/2);  new base A (0/5);  total (2/7)
Fisher's exact test for biased strand distribution p-value = 1.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAT  >  NZ_CP009273/340933‑341093
                                                                                |                                                                                
cATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAatat                                                                         <  1:283896/90‑1 (MQ=255)
  ttCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGc                                                                       <  1:223537/90‑1 (MQ=255)
                                            ttttttCTTTATCTTACGCATCCCACTAAAGCCTAAAAAAAAATATGCTGAAAGCCTAATATAAAAACCCGCCATTAGCTCATCAGGAag                             <  2:122157/88‑1 (MQ=255)
                                                ttCTTTATCTTCCCCACCGCACTCAAGCCTAAAAAAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCa                         <  1:142366/90‑1 (MQ=255)
                                                    gTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAgacg                     >  1:131747/1‑90 (MQ=255)
                                                         ttACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAAc                >  2:264841/1‑90 (MQ=255)
                                                               accccACTAAAGCCTAAAAAAAAATATGTTGTAAGCCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt          <  1:188716/86‑1 (MQ=255)
                                                                       cAAGCCTAAAAAAAAATATGTTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt  <  2:123601/90‑1 (MQ=255)
                                                                       cAAGCCTAAAAAAAAATATGCTGAAAGGCTAATAAAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt  <  2:281696/90‑1 (MQ=255)
                                                                                |                                                                                
CATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAT  >  NZ_CP009273/340933‑341093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑