Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092735,1620TA50.0% 29.0 / 11.4 30intergenic (+142/‑72)thrC/yaaXthreonine synthase/DUF2502 domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (15/0);  new base A (0/15);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.29e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAA  >  NZ_CP009273/5074‑5248
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tttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATa                                                                                       >  2:776106/1‑90 (MQ=255)
tttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATa                                                                                       >  1:1429105/1‑90 (MQ=255)
     gaagaaATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTGACTTAGAGATGAGGATTGCGGAGAATaacaac                                                                                  >  1:801765/1‑90 (MQ=255)
             tATGGAAAAAAAGGACAGGAAAAAAGGAAAAATTCTAAATAAATGCGTTAATTAAGAGATTAGGTTTGGGGAAAAAAACAACCGCCGTtc                                                                          <  1:776106/90‑1 (MQ=255)
                 gaaaaaaaGGAAAGGAAAAAAGAAAAAATTCACAAAAAATGGGTGAACTTAGAAATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCAt                                                                      <  1:1425822/87‑1 (MQ=255)
                 aaaaaaaaGAACGGGAAAAAAGGAAAAATTCCAAAAAAAGGCGGTAACTTAGAATTTGGGATGGCGGAAAAAAAAAACCGCCGTTCTCAt                                                                      <  2:904497/87‑1 (MQ=255)
                     aaaaTGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAg                                                                  >  2:1450010/1‑90 (MQ=255)
                       aaTGAGGGGAAAAAAGGAAAAATTCTAAATAAATGGGGTAATTTAGAGATGAGGTTGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTa                                                                <  1:589000/90‑1 (MQ=255)
                         gaaaaGGAAAAAGGGAAAATTTCAAAATAAGTGGGGTAATTAAGAGTTTGGGGGGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAAt                                                              <  1:1560502/86‑1 (MQ=255)
                          gACAGGAAAAAAGGAAAAATTCTAAAAAAATGCGGTAATTTAGAAATTAGGATTGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAAtc                                                             <  2:964410/90‑1 (MQ=255)
                           aCAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAAtct                                                            >  2:1425822/1‑90 (MQ=255)
                                   aaaGGAAAAATCCCAAAAAAAGGCGTTAACTAAAAGATTGGGATGGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGatat                                                    <  2:1443084/90‑1 (MQ=255)
                                    aaGGAAAAATTCTAAATAAATGGGGTAATTTAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                   <  2:408899/90‑1 (MQ=255)
                                        agaAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                               >  1:1399311/1‑90 (MQ=255)
                                        aaaaaTTCTAAAAAAATGGGGTAATTAAGAGATTAGGATGGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                               <  2:1317214/88‑1 (MQ=255)
                                            aTTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATa                                           >  2:721062/1‑90 (MQ=255)
                                                    aaaaTGGGGTAATTAAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                   <  2:406016/89‑1 (MQ=255)
                                                    aaaaTGCGGTAATTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                   <  2:121646/89‑1 (MQ=255)
                                                    aaaaTGCGGAAACTTAGATATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                   <  2:763082/89‑1 (MQ=255)
                                                               aCTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGa                        >  1:225869/1‑90 (MQ=255)
                                                                  tAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                     <  2:1243418/90‑1 (MQ=255)
                                                                  aaaagaTGAGGATGGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                     <  2:678199/87‑1 (MQ=255)
                                                                     agaTTAGGATGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAcc                  <  2:832582/90‑1 (MQ=255)
                                                                      gaTTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCt                 >  1:1334671/1‑90 (MQ=255)
                                                                        ttAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt               >  2:689076/1‑90 (MQ=255)
                                                                        ttAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt               >  2:1063359/1‑90 (MQ=255)
                                                                         tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg              >  2:1363764/1‑90 (MQ=255)
                                                                          aGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa             >  2:1135790/1‑90 (MQ=255)
                                                                                  ggAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg     >  1:1051545/1‑90 (MQ=255)
                                                                                     gaATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCaa  >  2:983327/1‑90 (MQ=255)
                                                                                        |                                                                                      
TTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAA  >  NZ_CP009273/5074‑5248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑