Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,525,9500TA62.2% 42.0 / 59.0 45intergenic (+102/+166)yjhR/BW25113_RS26295helicase YjhR/HNH endonuclease
Reads supporting (aligned to +/- strand):  ref base T (10/7);  new base A (16/12);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.42e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCAT  >  NZ_CP009273/4525827‑4526084
                                                                                                                           |                                                                                                                                      
tCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCt                                                                                                                          >  1:497385/1‑138 (MQ=255)
tCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCt                                                                                                                          >  2:763134/1‑138 (MQ=255)
tCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCt                                                                                                                          >  2:228802/1‑138 (MQ=255)
  tGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAAt                                                                                                                       >  2:638/1‑139 (MQ=255)
  tGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAAt                                                                                                                       >  1:590763/1‑139 (MQ=255)
  tGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAAt                                                                                                                       >  1:96805/1‑139 (MQ=255)
    gATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCa                                                                                                                     >  2:715201/1‑139 (MQ=255)
     aTCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCAt                                                                                                                    >  2:847991/1‑139 (MQ=255)
                cTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCa                                                                                                         >  1:341999/1‑139 (MQ=255)
                           atgaGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCt                                                                                               <  1:847991/138‑1 (MQ=255)
                              aGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGa                                                                                           >  1:428724/1‑139 (MQ=255)
                                     cATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATgg                                                                                    >  1:177915/1‑139 (MQ=255)
                                         aTACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCgg                                                                                 <  1:209539/138‑1 (MQ=255)
                                          tACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGt                                                                               <  1:660457/139‑1 (MQ=255)
                                             aGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCt                                                                            >  1:659715/1‑139 (MQ=255)
                                             aGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTcc                                                                                                               <  1:495190/104‑1 (MQ=255)
                                             aGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTcc                                                                                                               >  2:495190/1‑104 (MQ=255)
                                             aGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCt                                                                            >  1:772201/1‑139 (MQ=255)
                                                    gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCAtt                                                                                                                   <  2:519908/93‑1 (MQ=255)
                                                    gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCAtt                                                                                                                   >  1:519908/1‑93 (MQ=255)
                                                    gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTgg                                                                      >  2:433180/1‑138 (MQ=255)
                                                    gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTgg                                                                      >  1:785485/1‑138 (MQ=255)
                                                        aGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATga                                                                 <  2:237918/139‑1 (MQ=255)
                                                         gggCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATga                                                                 >  1:445909/1‑138 (MQ=255)
                                                            cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATgaaaa                                                              >  1:166789/1‑137 (MQ=255)
                                                            cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGAATgtaag                                                              >  2:646156/1‑138 (MQ=255)
                                                             atatTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCgg                                                                                 >  2:126934/1‑118 (MQ=255)
                                                             atatTATACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCgg                                                                                 <  1:126934/118‑1 (MQ=255)
                                                                    aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCt                                                                                                              >  1:453832/1‑82 (MQ=255)
                                                                    aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCt                                                                                                              <  2:453832/82‑1 (MQ=255)
                                                                    aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgca                                                      <  2:166789/138‑1 (MQ=255)
                                                                    aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgca                                                      <  2:177915/138‑1 (MQ=255)
                                                                    aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgca                                                      <  2:785485/138‑1 (MQ=255)
                                                                     ccAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaag                                                    <  2:426704/139‑1 (MQ=255)
                                                                     cagaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaag                                                    <  1:77446/136‑1 (MQ=255)
                                                                      cAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagc                                                   <  1:763134/139‑1 (MQ=255)
                                                                        aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                 <  1:433180/139‑1 (MQ=255)
                                                                        aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                 <  1:715201/139‑1 (MQ=255)
                                                                         tGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCt                                                                                                                          >  1:230992/1‑65 (MQ=255)
                                                                         tGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCt                                                                                                                          <  2:230992/65‑1 (MQ=255)
                                                                                                     aGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAGAAAAAGCAAGCAATAATATAAAAAAAGCCTAATTTCtttta                     >  1:709000/1‑136 (MQ=255)
                                                                                                     aGTCGCCTTTCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGAATGAAAAAAAAAGCAAACAATAATAAAAAAAAGGCCTAATttttttta                     >  1:432600/1‑136 (MQ=255)
                                                                                                              tCCTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTa            <  2:341999/138‑1 (MQ=255)
                                                                                                                cTGATTATAAAACTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAg          <  1:228802/138‑1 (MQ=255)
                                                                                                                       taAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGGAAAAAAATGCAAACAATAATATAAAAAAGGGCTAATTTCTTTTGAAATCATTTAACAtattat  >  1:694643/1‑139 (MQ=255)
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TCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCAT  >  NZ_CP009273/4525827‑4526084

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑