Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,556,2070TC30.8% 61.7 / 15.6 39S215G (AGT→GGT) rtcARNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (25/2);  new base C (0/12);  total (25/14)
Fisher's exact test for biased strand distribution p-value = 2.33e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCC  >  NC_000913/3556090‑3556343
                                                                                                                       |                                                                                                                                        
cACCGACGAAAAAAAAGCGTTCGGTGATATTTTCATTTTCGACTTAAAGCGAGACGGTATTCCCCGGCCCCT‑GGCCGCGGGGCAGGTTATGAATTTTCTGTTCATGCAGGAAAAAC‑CTCCCCGCCAGTGTAGCGATTTCa                                                                                                                    <  2:1165831/140‑1 (MQ=255)
  ccaacaacAAAAAAGCGTCCGGTATTTTTTTCTCTTTCAACTGCAAGGGGGAGGGTTTCCCCCCGCCCCG‑GGCCGGGGGGCGGGTTAGAAAAGTTGTTTTCATGGAGGAAAACT‑CCCCCCGCCAGTGTAGCGATTTCACg                                                                                                                  <  2:124839/134‑1 (MQ=255)
  ccGACGAAAAAAAAGCGTTGGGTAATTTTTTCATTTTCGACTTCAAGCGAGACGTTATCCCCCGGCCCCT‑GGTCGCGCGGAAGTTTATAAATATTCTGTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACg                                                                                                                  <  2:516650/140‑1 (MQ=255)
  ccGACAAAAAAAAAGCGTTGGGTGATTTTTTCCCTTTCGACTTCAAGGGAGACGTTATCCCCCGGCCCCT‑GGCCGCGCGGCAGGTTATGAATTTTCTGTACATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACg                                                                                                                  <  2:1162245/140‑1 (MQ=255)
  ccGACAAAAAAAAACGGTCGGGTGATTTTTCCACTTTCGATTACAAGAGAGCCGATATTCCCCGCCCCCG‑GGCCGGGCGGCAGGTAATAAATTTTCTGTCCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACg                                                                                                                  <  2:457166/140‑1 (MQ=255)
      cgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCa                                                                                                              >  1:828946/1‑140 (MQ=255)
       aaaaaaaaaGCGTGGGGTGATTTTTTCACTTTCGACTTCAAGCGAGAGGTTTTTCCCCGCCCCCT‑GGTCGCGCGGCAGTTTATAAATTTTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAg                                                                                                             <  2:1369648/137‑1 (MQ=255)
              aaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGAGGGTATTCCCCGGCCCCT‑GGTCGCGCGGCAGTTTATGAATTTTCTGTTCAGGGGGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATg                                                                                                      <  2:893992/140‑1 (MQ=255)
                   ttCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGcgcg                                                                                                 >  1:1022826/1‑140 (MQ=255)
                        tgtttttttCCCTTTCGCCTTCAAGCGAGACGTTATTCCCCGGCCCCG‑GGCCGCGCGGAAGTTTATGAATTTTCTGTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcaca                                                                                            <  2:40099/135‑1 (MQ=255)
                           ttttttCTCTTTCGACTTCAGGCGAGAC‑GTTTTTCCCGGCCCCTGGGTCGCGGGGCAGTTTATAAATTTTCTGTTCAGGCGGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCa                                                                                         <  2:668866/138‑1 (MQ=255)
                            tttttCACTTTCGATTTAAAGCAGGACGTTTTTCCCCGGCCCCG‑GGTCGCGGGGCGGGTTATAAATATTCTGTTAATGAAGGGAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAg                                                                                        <  2:909890/139‑1 (MQ=255)
                             ttttCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGc                                                                                       >  1:341715/1‑140 (MQ=255)
                                  aCTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATa                                                                                  >  1:1281923/1‑140 (MQ=255)
                                     tccGACTACAAGCGAGCCGGTATTCCCCGGCCCCG‑GGCCGCGCGGCAGTTTATAAATTTTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGaa                                                                               <  2:248358/138‑1 (MQ=255)
                                             aaaGCGAGGCGTTATTCCCCGCCCCTG‑GGTCGCGCGGCGGTTTATAAATATTCTGTTCATGCAGGGAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa                                                                       <  2:795040/139‑1 (MQ=255)
                                             aaaGCGAGAGGTTATTCCCCGCCCCCT‑GCGCGCGCGGGGGATTATAAATTTTCTTTTCGGGCAGGAAAACC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa                                                                       <  2:828946/139‑1 (MQ=255)
                                                         tatcccccGCCCCCG‑GGTCGCGCGGCAGGTTATGAATATTCTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcaca                                                           <  2:1281923/135‑1 (MQ=255)
                                                                  gCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcg                                                  >  1:1374364/1‑140 (MQ=255)
                                                                   ccccT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                                 >  1:1067015/1‑140 (MQ=255)
                                                                   ccccT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                                 >  1:1175726/1‑140 (MQ=255)
                                                                   ccccT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                                 >  1:755546/1‑140 (MQ=255)
                                                                   ccccT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                                 >  1:342842/1‑140 (MQ=255)
                                                                       cgggccgcgcgGCGGTTTATAAATTTTCTTTTCATG‑AGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCt                                              <  2:755546/135‑1 (MQ=255)
                                                                          gTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGc                                           >  1:201641/1‑140 (MQ=255)
                                                                              cgcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                       >  2:852949/1‑140 (MQ=255)
                                                                                cgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGtt                                     >  1:223835/1‑140 (MQ=255)
                                                                                cgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGtt                                     >  1:39377/1‑140 (MQ=255)
                                                                                  gCAGTTTATAAATATTCTGTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGc                                   <  2:1067015/140‑1 (MQ=255)
                                                                                   gggtttATAAATTTTCTGTTCA‑GGAGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                  <  2:1374364/136‑1 (MQ=255)
                                                                                   gaGGTTATAAATTTTCTTTTAATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                  <  2:1022826/139‑1 (MQ=255)
                                                                                   cAGGTTATGAATATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                  <  1:424762/140‑1 (MQ=255)
                                                                                          taaaTATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGtt                           <  1:398078/138‑1 (MQ=255)
                                                                                                ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGa                     >  1:759410/1‑140 (MQ=255)
                                                                                                ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGa                     >  1:392464/1‑140 (MQ=255)
                                                                                                 tCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGAt                    >  2:1323105/1‑140 (MQ=255)
                                                                                                 tCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAACTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGAt                    >  2:214244/1‑140 (MQ=255)
                                                                                                   tGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGc                  >  1:535131/1‑140 (MQ=255)
                                                                                                    gTTCATGCAGGGAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                  <  1:1362995/123‑1 (MQ=255)
                                                                                                    gTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                  >  2:1362995/1‑123 (MQ=255)
                                                                                                    gTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGcc                 >  2:535027/1‑140 (MQ=255)
                                                                                                     ttCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa                >  2:522566/1‑140 (MQ=255)
                                                                                                     ttCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa                >  1:962145/1‑140 (MQ=255)
                                                                                                     ttCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa                >  1:542970/1‑140 (MQ=255)
                                                                                                      tCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCAc               >  1:284572/1‑140 (MQ=255)
                                                                                                               gAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGAc      >  2:469097/1‑140 (MQ=255)
                                                                                                                   aa‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTcc  <  2:342842/140‑1 (MQ=255)
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CACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCT‑GGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCC  >  NC_000913/3556090‑3556343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑