Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,734,2690TG51.5% 22.8 / 44.3 33V402G (GTG→GGG) avtAvaline‑‑pyruvate transaminase
Reads supporting (aligned to +/- strand):  ref base T (3/13);  new base G (17/0);  total (20/13)
Fisher's exact test for biased strand distribution p-value = 9.77e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.30e-06
Rejected as consensus: Frequency below/above cutoff threshold.

CAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATT  >  NZ_CP009273/3734185‑3734358
                                                                                    |                                                                                         
cAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGaaaa                                                                                      >  1:414392/1‑88 (MQ=255)
 aGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGAt                                                                                     >  1:96714/1‑90 (MQ=255)
       ggATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGc                                                                               >  2:312572/1‑90 (MQ=255)
            aaCCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAag                                                                          <  1:50232/90‑1 (MQ=255)
            aaCCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAag                                                                          <  2:438996/90‑1 (MQ=255)
            aaCCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAag                                                                          <  1:312572/90‑1 (MQ=255)
            aaCCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAag                                                                          <  1:408361/90‑1 (MQ=255)
                gTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGAt                                                                      <  1:104932/90‑1 (MQ=255)
                 tGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGGAGATTCTGGGGGGAGAGAtt                                                                     >  2:345590/1‑89 (MQ=255)
                 tGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTTGCGGGAGAGATa                                                                     >  2:292581/1‑90 (MQ=255)
                 tGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATa                                                                     >  2:252033/1‑90 (MQ=255)
                           cGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCt                                                           <  1:252033/90‑1 (MQ=255)
                                 aaTGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTg                                                     >  2:84125/1‑90 (MQ=255)
                                      aTGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGt                                                <  2:362446/90‑1 (MQ=255)
                                      aTGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGt                                                >  1:190326/1‑90 (MQ=255)
                                       tGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTTTGGGGGGAGGGGTAGAAAAAGCCCGGGCTGGAAGtt                                               >  2:66615/1‑89 (MQ=255)
                                       tGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTc                                               >  1:49710/1‑90 (MQ=255)
                                        gcgcATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAAAGCCTGGGCTGAAAGTCa                                              >  2:68969/1‑90 (MQ=255)
                                            aTGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGCAAAAATAGAAAAAGCCTGGGGCGAAAGTCACTaa                                          >  2:118326/1‑90 (MQ=255)
                                            aTGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGGGATAGAAAGAGCCTGGGGTGAAAGTCACTaa                                          >  1:28692/1‑90 (MQ=255)
                                                   aCGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGaaa                                                                 <  1:410087/60‑1 (MQ=255)
                                                   aCGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGGAGAGAAAAAAAAAACCTGGGGTGGAAGTCAATAAAAAATGc                                   >  2:397403/1‑90 (MQ=255)
                                                   aCGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGaaa                                                                 >  2:410087/1‑60 (MQ=255)
                                                       aCCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGa                               <  1:292581/90‑1 (MQ=255)
                                                           gagCCGGAGAAAATTGAGGCGGGGGGGAAGATTTTGGCGGGAGAGATAGAAAGAGGCTGGGGTGGAAGAGACTAAAAAATGCCTGATgcg                           >  2:389490/1‑90 (MQ=255)
                                                           gagCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATgcg                           >  2:227425/1‑90 (MQ=255)
                                                            agCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATgcgc                          <  2:336942/90‑1 (MQ=255)
                                                             gCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATGCGCt                         >  1:8417/1‑90 (MQ=255)
                                                                ggAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGGTGAAAGTCACTAAAAATTGCCTGATGCGCTACg                      >  2:141347/1‑90 (MQ=255)
                                                                 gagaAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCTCTAAAAATTGCCTGATGCGCTACGc                     <  1:389490/90‑1 (MQ=255)
                                                                           aGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCt                                                           <  2:153300/42‑1 (MQ=255)
                                                                           aGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCt                                                           >  1:153300/1‑42 (MQ=255)
                                                                               gggggTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACa       <  1:84125/90‑1 (MQ=255)
                                                                                    tGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGAtt  <  1:128258/90‑1 (MQ=255)
                                                                                    |                                                                                         
CAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATT  >  NZ_CP009273/3734185‑3734358

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: