Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,379,0450TG53.3% 4.0 / 11.6 15G224G (GGT→GGG) ycjXYcjX family protein
Reads supporting (aligned to +/- strand):  ref base T (1/6);  new base G (8/0);  total (9/6)
Fisher's exact test for biased strand distribution p-value = 1.40e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAGGCCGATAAGCATACCAAT  >  NZ_CP009273/1378988‑1379129
                                                         |                                                                                    
gCAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCCCGCCGCAATTCTTCCCCTGGCCggg                                                      >  1:178127/1‑89 (MQ=255)
 cAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCAGa                                                      <  1:235004/89‑1 (MQ=255)
 cAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCAGa                                                      >  2:235004/1‑89 (MQ=255)
 cAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCTGCAATTCTTCCCGTGGCCgggt                                                     >  2:167536/1‑88 (MQ=255)
   ggggCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCTGCAATTCTTCCCCTGGCCgggggt                                                   >  1:165337/1‑86 (MQ=255)
   ggggCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCCGCAATTCTTCCCGTGGCCGGATGt                                                   >  2:197382/1‑90 (MQ=255)
       cTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGAt                                               <  2:253689/90‑1 (MQ=255)
        tGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCCGCGATTCTTCCCCCGGCCCGGTGTCGGTa                                              >  1:231731/1‑90 (MQ=255)
               tATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTgggg                                       >  2:227656/1‑90 (MQ=255)
                      ccTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGGGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTcc                                >  1:112113/1‑90 (MQ=255)
                                  gTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCCGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAg                    <  1:197382/90‑1 (MQ=255)
                                            gagaTATGGCAGGGGCGCCCGCGCTGCAATTTTTCCCCTGGCCGGGTGTTGATACCTGGGGGGGGGCCCAACTGGCGCAGGCCGGTaaac          >  1:305472/1‑88 (MQ=255)
                                                  tGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAGGCCGATAAGCATACCa    <  2:178127/90‑1 (MQ=255)
                                                    gCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAGGCCGATAAGCATACCAAt  <  2:169394/90‑1 (MQ=255)
                                                    gCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAGGCCGATAAGCATACCAAt  <  2:309962/90‑1 (MQ=255)
                                                         |                                                                                    
GCAGGGGCTGCACTTTATTCAGCCTGGGCGCTTTGTCTTGCCGGGAGATATGGCAGGTGCGCCCGCGCTGCAATTCTTCCCGTGGCCGGATGTCGATACCTGGGGCGAGTCCAAACTGGCGCAGGCCGATAAGCATACCAAT  >  NZ_CP009273/1378988‑1379129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑