Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,860,9020CT20.0% 55.9 / 10.1 30Q3Q (CAG→CAA) rpoSRNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base C (13/11);  new base T (3/3);  total (16/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.61e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTT  >  CP009273/2860757‑2861045
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gtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGa                                                                                                                                              <  2:722073/149‑1 (MQ=255)
       tCCCTTCGATAACAGTTCCGATTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCACCTTCATTTAAAGCATGAACTTTCAGCGTATTCTGACTCATaa                                                                                                                                       <  2:134995/149‑1 (MQ=255)
         ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTGATCGTATTCTGACTCGTAAgg                                                                                                                                     >  1:606250/1‑149 (MQ=255)
            gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATATAAATCATAAACTTTCAGCGAAATCTGACTCATAAGGtaa                                                                                                                                  >  2:613057/1‑147 (MQ=255)
              gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCt                                                                                                                                <  2:659735/149‑1 (MQ=255)
                          tcgtCGGCCAAATCGTTATCACCGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGAt                                                                                                                    <  2:502408/146‑1 (MQ=255)
                             tCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTGAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATccc                                                                                                                 <  1:493711/149‑1 (MQ=255)
                               ggCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCtt                                                                                                               <  2:165678/149‑1 (MQ=255)
                                   aaaTCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGAGGCTCCTACCCGTGAGCCCTTGACg                                                                                                           >  1:621166/1‑149 (MQ=255)
                                               cTGGGTTCCTGTTCCACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTTTCCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGc                                                                                               <  1:574931/149‑1 (MQ=255)
                                                   gTTCCTGTGCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCaaca                                                                                           <  2:716794/149‑3 (MQ=255)
                                                    ttCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCTCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAg                                                                                          >  1:390728/1‑149 (MQ=255)
                                                    ttCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAg                                                                                          >  1:122358/1‑149 (MQ=255)
                                                    ttCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAg                                                                                          >  1:122389/1‑149 (MQ=255)
                                                        tGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAGTTAAATCATGAACTATCAGCGTCTTCTGACTCCTAAGGAAGCTACAACCAATGATCCCTTGACTGAAGATGCAAGCAGAATCCTg                                                                                      >  2:326898/1‑149 (MQ=255)
                                                           tCTACTAAGGCCCTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACGTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGtt                                                                                   <  2:681523/149‑1 (MQ=255)
                                                                  aGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGa                                                                            >  1:109183/1‑149 (MQ=255)
                                                                    gCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGAtc                                                                          >  1:178351/1‑148 (MQ=255)
                                                                     ccTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGCTCCCTTGCCGGAACATTCAAGCAAAAGCCTGGTTCCGCCGAttt                                                                         >  2:645258/1‑149 (MQ=255)
                                                                       ttttCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTAt                                                                       <  2:101438/149‑1 (MQ=255)
                                                                                   aCCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCaaa                                                           <  2:122389/149‑1 (MQ=255)
                                                                                   aCCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCaaa                                                           <  2:122358/149‑1 (MQ=255)
                                                                                   aCCTCAACTCCGTTCTCATCAAATTCCCCATCTTCATTTAAATCATGAACTTTCAGCGTATTTTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCaaa                                                           <  2:390728/149‑1 (MQ=255)
                                                                                           tCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAACAAAAGCCTGGTTTCGCCGATTTATCGCTTCGGCAAATaagccag                                                   >  2:2999/1‑144 (MQ=255)
                                                                                                              gCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTAACGCAGAAGCCTGGTTTCGCCGATGTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTcccc                                >  2:629083/1‑149 (MQ=255)
                                                                                                                          aaaTCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAAtt                    >  1:224346/1‑149 (MQ=255)
                                                                                                                                     tttCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCaa         >  1:298791/1‑149 (MQ=255)
                                                                                                                                     tttCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCaa         >  1:699314/1‑149 (MQ=255)
                                                                                                                                          gCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCgtg    >  1:496809/1‑149 (MQ=255)
                                                                                                                                            gTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGtt  <  1:357619/149‑1 (MQ=255)
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GTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTT  >  CP009273/2860757‑2861045

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑