Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273997,4470TG53.8% 23.6 / 35.0 26V62G (GTA→GGA) elfGfimbrial protein
Reads supporting (aligned to +/- strand):  ref base T (2/10);  new base G (14/0);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 1.24e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.27e-04
Rejected as consensus: Frequency below/above cutoff threshold.

CGGGCAGTGTCATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGTGGCCGAT  >  NZ_CP009273/997358‑997536
                                                                                         |                                                                                         
cGGGCAGTGTCATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGt                                                                                           <  1:784968/90‑1 (MQ=255)
  ggCAGTGTCATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAg                                                                                         >  2:146312/1‑90 (MQ=255)
      gtgtCATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTaa                                                                                     >  2:618305/1‑90 (MQ=255)
          cATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGAc                                                                                 <  2:162913/90‑1 (MQ=255)
                actCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAAAAAAAttt                                                                           >  1:942250/1‑90 (MQ=255)
                  tCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTa                                                                         <  1:33368/90‑1 (MQ=255)
                  tCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGGGTTTAAGAAAAAttttt                                                                         >  1:685550/1‑89 (MQ=255)
                     ggggAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTa                                                                                      <  2:429889/74‑1 (MQ=255)
                     ggggAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTa                                                                                      >  1:429889/1‑74 (MQ=255)
                        gAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTa                                                                                      >  2:317474/1‑71 (MQ=255)
                        gAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTa                                                                                      <  1:317474/71‑1 (MQ=255)
                        gAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGAAAAAATTTATCAGTg                                                                   >  1:336880/1‑90 (MQ=255)
                          aTCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGGGGTTAAGAAAAAATTTTTCAGTggg                                                                 >  1:887877/1‑89 (MQ=255)
                          aTCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAATTTTTTCAGTGGa                                                                 >  2:473269/1‑90 (MQ=255)
                                     ggCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAAcgaatcgaat                                                      <  1:580043/90‑1 (MQ=255)
                                        gTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGat                                                   >  2:597215/1‑90 (MQ=255)
                                        gTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAAAAAAATTTTTTTAGGGGAACGAAACGAATGat                                                   >  1:540982/1‑90 (MQ=255)
                                         tCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAAATTTTTTAGGGGGACGAAACGAAAGaat                                                  >  1:283279/1‑88 (MQ=255)
                                          cAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTTTCAGTGGAACGAAACGAATGatta                                                 >  1:324256/1‑90 (MQ=255)
                                                  gCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGttt                                         >  2:894844/1‑90 (MQ=255)
                                                             cTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGc                              >  2:480530/1‑90 (MQ=255)
                                                                 aggaAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATa                          <  2:22529/90‑1 (MQ=255)
                                                                     agaagCAAATACGGCAGGGGGAGTTAAAGACAAATTTTTTCAGGGGAAAGAATCGAATGATTATTATGTTTTCTGTGATTGCGATaaaaa                      >  1:229648/1‑88 (MQ=255)
                                                                       aagCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACa                    <  2:113554/90‑1 (MQ=255)
                                                                       aagCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACa                    <  1:618305/90‑1 (MQ=255)
                                                                       aagCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACa                    <  2:942250/90‑1 (MQ=255)
                                                                                       ggTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGTGGCCg    <  1:146312/90‑1 (MQ=255)
                                                                                         tAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGTGGCCGAt  <  2:887877/90‑1 (MQ=255)
                                                                                         |                                                                                         
CGGGCAGTGTCATACTACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGTGGCCGAT  >  NZ_CP009273/997358‑997536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑