Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,125,8350AC58.3% 19.9 / 28.1 24V162G (GTA→GGA) flgAflagellar basal body P‑ring formation chaperone FlgA
Reads supporting (aligned to +/- strand):  ref base A (9/1);  new base C (0/14);  total (9/15)
Fisher's exact test for biased strand distribution p-value = 7.65e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-05
Rejected as consensus: Frequency below/above cutoff threshold.

GCTGCATTGTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGTTGATTG  >  NZ_CP009273/1125751‑1125921
                                                                                    |                                                                                      
gCTGCATTGTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGc                                                                                   >  2:428581/1‑90 (MQ=255)
             gcgcCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGaa                                                                      >  2:34207/1‑90 (MQ=255)
                  tGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTgg                                                                 >  2:720133/1‑90 (MQ=255)
                  tGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTgg                                                                 >  1:719957/1‑90 (MQ=255)
                      cTTCTGGGTTGGCGCTAACCCCATCCCCGCGGGCGATCACATTGACGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTa                                                             <  2:111834/90‑1 (MQ=255)
                         cTGCGTGGGCGCAAACCCCACCCCCGGGGGCGATCACATGGACGTGTTGCCCCGCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACt                                                          <  1:101907/90‑1 (MQ=255)
                            ctttGGCGCAAACCCCATCCCCGCTGGCGATCACATTGACGCGTTGCCCCGTTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGa                                                       <  2:38721/88‑1 (MQ=255)
                            cGTTGGCGCAAACCCCACCCCCGCGGGCAATCACTTTGCCGCGTTGCCCCTTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGa                                                       <  1:190596/90‑1 (MQ=255)
                             gtgggCGCAAACCCCATCCCCGCTGGCGATCACATTGGCGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGAt                                                      <  2:737842/87‑1 (MQ=255)
                              ttGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATa                                                     >  1:289988/1‑90 (MQ=255)
                               tGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAg                                                    >  1:6080/1‑90 (MQ=255)
                                  cgcTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGtt                                                 >  1:81560/1‑90 (MQ=255)
                                      aaccccACCACCGGGGGGAATCACTTTGCCGTGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATc                                             <  1:34207/87‑1 (MQ=255)
                                      aaaCCCATCCCCGCGGGCAATCACTTTGACGCGTTGCCCCTTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATc                                             <  1:274214/90‑1 (MQ=255)
                                       cacccacccCCGCGGGTGTCCACATTGCCGCTTTCCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCg                                            <  1:720133/89‑1 (MQ=255)
                                             tCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGAt                                      >  1:444925/1‑90 (MQ=255)
                                                ccGCTGGCGATCACTTTGACGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGa                                   <  2:194123/90‑1 (MQ=255)
                                                      gCGATCACATTGCCGCGTTGTCCCGCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc                             <  2:64255/90‑1 (MQ=255)
                                                      gCGATCACATTGCCGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc                             <  2:289988/90‑1 (MQ=255)
                                                      gCGATCACATTGCCGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc                             <  2:568294/90‑1 (MQ=255)
                                                      gCGATCACATTGACGCGTTGTCCCTTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc                             <  2:72942/90‑1 (MQ=255)
                                                        gATCACTTTGCCGGGTTGTCCCTCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAg                           <  2:46402/90‑1 (MQ=255)
                                                                                ttttCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGttgatt   <  1:191578/90‑1 (MQ=255)
                                                                                 tttACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGttgattg  >  2:637742/1‑90 (MQ=255)
                                                                                    |                                                                                      
GCTGCATTGTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGTTGATTG  >  NZ_CP009273/1125751‑1125921

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑