Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,455,6040GA53.8% ‑2.1 / 11.4 13R132C (CGC→TGC) treBPTS trehalose transporter subunit IIBC
Reads supporting (aligned to +/- strand):  ref base G (5/1);  new base A (0/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.59e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGC  >  NZ_CP009273/4455534‑4455689
                                                                      |                                                                                     
gTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAAccg                                                                    >  1:397299/1‑90 (MQ=255)
gTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAAccg                                                                    >  2:207360/1‑90 (MQ=255)
      aGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTa                                                              >  2:261951/1‑90 (MQ=255)
        ggAGGGTTACATTTGCGCCAGCGTCTGACCGTTGCTCAGGGGCAAACCGCCGATCGCATTGCAAAAACCGAGGATAAAACCGCCGCTAAt                                                            <  1:356851/90‑1 (MQ=255)
             ggTAAATTGGCGCCAGCGTCTGACCGTTGCTAATGGGAAAACCGCCGATCACATTGCAAAAACGGAGGATCAAACCGCCGCTAATCAAcg                                                       <  2:329061/90‑1 (MQ=255)
                 cATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCggg                                                   >  2:356851/1‑90 (MQ=255)
                         ccAGCGTCTGCCCGTTCCTCGGGGGAAAACCGCCGATCACATGGAAAAAACCGAGGATAAACCCGCCGCTAATCAACGCGGGCAGCAACg                                           <  2:277327/90‑1 (MQ=255)
                            gCGTCGGCCGGTTCCTCAGGGAAAAATCCCCGATCAAATGGAAAAACCAGAGAAACAAACCGCCGCTAATCAACGCGGGCAGCAACGGga                                        <  2:338253/90‑1 (MQ=255)
                                               ggaaaaaCCGCCGATCACATTGCAAAAACCGAGGAAAAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATg                     <  2:55320/86‑1 (MQ=255)
                                                    aaTCGCCAATCACATTGCAAAACCCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATgagaga                <  1:50099/90‑1 (MQ=255)
                                                          cGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAAc                                            <  1:5790/56‑1 (MQ=255)
                                                          cGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAAc                                            >  2:5790/1‑56 (MQ=255)
                                                                  ttGCAAAACCCGAGAAACAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGc  <  1:168245/90‑1 (MQ=255)
                                                                      |                                                                                     
GTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGC  >  NZ_CP009273/4455534‑4455689

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑