Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,134,4070AC54.5% 8.8 / 11.9 11G229G (GGT→GGG) asmAouter membrane assembly protein AsmA
Reads supporting (aligned to +/- strand):  ref base A (3/2);  new base C (0/6);  total (3/8)
Fisher's exact test for biased strand distribution p-value = 6.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGAT  >  NZ_CP009273/2134339‑2134491
                                                                    |                                                                                    
ttATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAAtt                                                                 <  2:470584/90‑1 (MQ=255)
              ccACTGGGCCTGGAACCCCCCCTCCCCCTGAATACCTTGTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAgccgc                                                   <  2:199204/90‑1 (MQ=255)
                     gCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTaaa                                            >  2:225918/1‑90 (MQ=255)
                             aCTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCgg                                    >  1:111772/1‑90 (MQ=255)
                                     ccccctgAATCCCTTTTTTTGGAAAACCGCCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAg                            <  1:524290/89‑1 (MQ=255)
                                          tgAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCa                       <  2:111772/90‑1 (MQ=255)
                                               cccTTTTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtac                  <  2:166381/89‑1 (MQ=255)
                                                  ttGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgt               >  1:127263/1‑90 (MQ=255)
                                                   tGTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgta              <  2:228564/90‑1 (MQ=255)
                                                    gTTTGGGAAATTCGCCCCCCGCCAACTCCCAGTTAATTTGTAAAATACCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgtac             <  1:240543/90‑1 (MQ=255)
                                                               tCGGCCCCCTGCAACTGCCATTTAATTTGTTAAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGat  <  2:127263/90‑1 (MQ=255)
                                                                    |                                                                                    
TTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGAT  >  NZ_CP009273/2134339‑2134491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑