Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273341,0390CA58.3% 0.2 / 17.3 12intergenic (+337/‑76)BW25113_RS01680/BW25113_RS01685hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (5/0);  new base A (0/7);  total (5/7)
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.

TGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTC  >  NZ_CP009273/340968‑341123
                                                                       |                                                                                    
tgtgtgGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCtc                                                                    >  2:354761/1‑90 (MQ=255)
              tCTGTATTTTACGCATCGCACTCAAGCCTGAAAAAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAg                                                      <  1:266308/90‑1 (MQ=255)
                  tATCTTCCCCACCGCACTCAACCCTGAAAAAAAATATGCTGAAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAgacga                                                  <  1:314318/90‑1 (MQ=255)
                            aTCGCACTCAACCCTGAAAAAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt                                        <  1:343152/90‑1 (MQ=255)
                             tCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAtt                                       >  1:136267/1‑90 (MQ=255)
                             tCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAtt                                       >  1:265310/1‑90 (MQ=255)
                                 cctaaaGCCTGACAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgttg                                   <  1:182050/86‑1 (MQ=255)
                                   taaaGCCTGAAAAAAAATATGTTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTa                                 <  1:5959/88‑1 (MQ=255)
                                    aaggCCTGAAAAAAAATATGTTGTAGGCCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt                                <  1:300619/87‑1 (MQ=255)
                                                   atatGCTGAAAGCCACATAAAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAg                 <  2:136267/90‑1 (MQ=255)
                                                               gCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCg     >  2:99178/1‑90 (MQ=255)
                                                                  cATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTc  >  1:79381/1‑90 (MQ=255)
                                                                       |                                                                                    
TGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTC  >  NZ_CP009273/340968‑341123

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: ‑