Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,134,4070AC54.2% 17.5 / 32.7 24G229G (GGT→GGG) asmAouter membrane assembly protein AsmA
Reads supporting (aligned to +/- strand):  ref base A (9/2);  new base C (0/13);  total (9/15)
Fisher's exact test for biased strand distribution p-value = 4.21e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.89e-05
Rejected as consensus: Frequency below/above cutoff threshold.

TAAATGAAAGGCGTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGAT  >  NZ_CP009273/2134325‑2134491
                                                                                  |                                                                                    
tAAATGAAAGGCGTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCa                                                                               <  2:125658/90‑1 (MQ=255)
       aaGGCGTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCa                                                                        >  1:451022/1‑90 (MQ=255)
            gTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTaa                                                                   >  2:774648/1‑90 (MQ=255)
            gTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTaa                                                                   >  1:473861/1‑90 (MQ=255)
              ttATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAAtt                                                                 <  2:451022/90‑1 (MQ=255)
                          tGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAgcc                                                     >  1:778398/1‑90 (MQ=255)
                          tGCCACGGGGCCTGGAAACCCCCCTGCCCCTGAATACTTTGTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAgcc                                                     <  2:339891/90‑1 (MQ=255)
                          cgCCACGGGGCCGGAAACCCCCCCTCCCCCTAAATCCTTTTTTTTGGAAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAgcc                                                     <  1:169529/89‑1 (MQ=255)
                             cACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAgccgcc                                                  >  1:160163/1‑90 (MQ=255)
                                       ggAACCCCCCCTGCCCCTGAATACCTTTTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCAt                                        <  2:499976/90‑1 (MQ=255)
                                       ggAAACTCCCCTGCCCCTGAATCCCTTGTTTTGGTAAATCGGCCCCCTCCAACTGCCAGTTAATTTGTTAAATAGCCGCCGTTAAATCAt                                        <  2:595471/90‑1 (MQ=255)
                                           aCTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCgg                                    >  2:171833/1‑90 (MQ=255)
                                            cccccctgcccctgAATCCCTTGTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGa                                   <  2:473861/88‑1 (MQ=255)
                                                  tgcccctgAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCa                             >  1:571768/1‑90 (MQ=255)
                                                        taaaTCCCTTTTTTTGGAAAACCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCa                       <  2:183713/88‑1 (MQ=255)
                                                        taaaTACTTTTTTTTGGTAAATCGGCCCCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCa                       <  2:327759/88‑1 (MQ=255)
                                                             aCCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtac                  >  2:602536/1‑90 (MQ=255)
                                                              ccTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtacc                 >  1:435703/1‑90 (MQ=255)
                                                                 ttttttGGTAAATCGGCCCCCTGCACCTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgta              <  2:160163/88‑1 (MQ=255)
                                                                 ttttttGGAAAATCGGCCCCCTGCAACTGCCATTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgta              <  2:778398/88‑1 (MQ=255)
                                                                   ttttGGAAAATCGCCCCCCTGCAACTGCCAGTTAATTTGTTAAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCtaccgtacc            <  2:681946/90‑1 (MQ=255)
                                                                         aaaaTCGGCCCCCTGCAACTGCCAGTTAATTTTTTAAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAg      <  2:626944/89‑1 (MQ=255)
                                                                         aaaaTCGGCCCCCTCCACCTGCCAGTTAATTTTTTAAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAg      <  1:537890/89‑1 (MQ=255)
                                                                             tCGGCCCCCTGCAACTGCCAGTTATTTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGat  <  1:539605/90‑1 (MQ=255)
                                                                                  |                                                                                    
TAAATGAAAGGCGTTTATGTGACTCCTGCCACTGGGCCTGGAAACTCCCCTGCCCCTGAATACCTTGTTTTGGTAAATCGGCACCCTGCAACTGCCAGTTAATTTGTTCAATAGCCGCCGTTAAATCATGCGGATAATCAGAAGCATCTACCGTACCGTTAAGGGAT  >  NZ_CP009273/2134325‑2134491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑