Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,346,6530CA45.8% 24.0 / 11.1 24L30F (TTG→TTT) gmrcyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability
Reads supporting (aligned to +/- strand):  ref base C (12/1);  new base A (0/11);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 9.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGATGCACAGAAAGATCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGTCCGCGGTTAAATAAAAGGAACAACATGACT  >  NC_000913/1346506‑1346801
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cAGATGCACAGAAAGATCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCaa                                                                                                                                                    >  2:112936/1‑150 (MQ=255)
  gATGCACAGAAAGATCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAAc                                                                                                                                                 <  1:655994/151‑1 (MQ=255)
             aGATCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCttt                                                                                                                                      >  1:391775/1‑151 (MQ=255)
               aTCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTcc                                                                                                                                    >  2:845952/1‑151 (MQ=255)
                      tCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAAcc                                                                                                                             >  2:817273/1‑151 (MQ=255)
                        aTCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGc                                                                                                                           >  1:193400/1‑151 (MQ=255)
                             cGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGt                                                                                                                       >  2:527860/1‑150 (MQ=255)
                               gTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATg                                                                                                                    >  1:227668/1‑151 (MQ=255)
                                        atcatcaGGCTGGGGGTAATGACCGTCTTTCCCCTGAGGCGGGCAGCCTGTTCGGAAGAAAACTGAAATGTACGATCAGGTTCTGTGTTTGCGGTGGTAAAAAAGCAAAAAACATCGCTGTTTTCCTCAAACCGCCAGTATgg                                                                                                                   <  2:234362/143‑1 (MQ=255)
                                           atcaGGCGGGGGGTGAGGCCCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGAAATGTACGATCGGGTTTTGTGTTTGGGGTGGTAAAAAAGCGAAAAACATCGCTGTTTTCCGTCAACCGCCAGTATGGATTGTGCGATc                                                                                                        <  1:610574/151‑1 (MQ=255)
                                                                gTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTtg                                                                                   >  2:338012/1‑151 (MQ=255)
                                                                            aggCGAGCAGCCTTTTCGGCAGATAACTGCAATGTCCGATCAGGTTCTGTGGTTTGGGTGGTAAAAAAGCAAAAAACATCGCTGTTTCCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTa                                                                        <  1:751464/148‑1 (MQ=255)
                                                                              gCGAGCAGCTTGTTGGGCAAATAACTGAAATGTACGATCGGTTTTTGTGTTTTGGGGGGAAAAAAAGCGAAAAACATCGCTGTTTCCCGTAAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTccc                                                                          <  1:112961/146‑1 (MQ=255)
                                                                                gAGCGGCTTGTTCGGAAGATAACTGCATTGTACGATCAGGTTCTGTGTTTTGGGTGGAAAAAAGGCAAAAAACATCGCTGCTTTCCGTAAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAAc                                                                      <  1:784860/148‑1 (MQ=255)
                                                                                     gcCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTc                                                               >  1:285695/1‑150 (MQ=255)
                                                                                       cTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCatg                                                            >  2:671988/1‑151 (MQ=255)
                                                                                           tCGGAAGATAACTGCAATGTACGATCGGTTTCTGTGTTTTCGGTGGTAGAAAAGCGAAAAACATCGCTGCTTCCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCatgatg                                                         <  1:19137/150‑1 (MQ=255)
                                                                                             ggaaaaTAACTGCAATGTACGATCAGTTTTTGTGTTTTCGGTGGAAAAAAAGCGAAAAACAGCGTTGTTTCCCGACAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCatgatg                                                         <  2:417796/143‑1 (MQ=255)
                                                                                              gaaGATAACGGCAATGTACGACCGGGTTCGGTGTTTTGGGGGGAAGAAAAGCGAAAAACATCGCTGCTTTCCTCAAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCa                                                       <  2:52471/147‑1 (MQ=255)
                                                                                                aaaTAACTGAAATGTACGATCTGGTTTTGTGTTTTCGGTGGAAAAAAACCGAAAAACATCCCTTCTTCCCTTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCa                                                       <  2:401354/145‑1 (MQ=255)
                                                                                                         aattgcaCGATTAGGTTCTGTGGTTTCGGTGGTAGAAAAGAGAAAAACCTCGCTGCTTTCCGTAAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGt                                            <  1:31118/143‑1 (MQ=255)
                                                                                                                   tCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGt                                >  2:276697/1‑151 (MQ=255)
                                                                                                                            gtgtTTTGGGTGGTAAAAAAGCTAAAAACCGCGTTCTTTTCCGTAAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGTCCGCGGtt                        <  2:865578/150‑1 (MQ=255)
                                                                                                                                tttCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGTCCGCGGTtaaat                    >  1:388649/1‑150 (MQ=255)
                                                                                                                                                 cgcAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGTCCGCGGTTAAATAAAAGGAACAACATGACt  >  1:604620/1‑151 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
CAGATGCACAGAAAGATCGCTTTCATCGACGGTCAGACTCATCATCAGGCTGGAGGTGATGACCGTCATTTCCCTGATGCGAGCAGCCTGTTCGGCAGATAACTGCAATGTACGATCAGGTTCTGTGGTTTCGGTGGTAGAAAAGCGCAAAACATCGCTGCTTTCCGTCAACCGCCAGTATGGATTGTGCGATCCGAGAAAGTTGTACAACGTTGTGGACTCCCTAACGGTTTTCATGATGCATATCCTCCGGTTAACAGCGGAGTCCGCGGTTAAATAAAAGGAACAACATGACT  >  NC_000913/1346506‑1346801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑