Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913593,9930TG51.4% 46.1 / 58.8 35T260P (ACC→CCC) cusScopper‑sensing histidine kinase in two‑component regulatory system with CusR
Reads supporting (aligned to +/- strand):  ref base T (1/16);  new base G (18/0);  total (19/16)
Fisher's exact test for biased strand distribution p-value = 4.19e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.88e-07

GCGTCAGCTCTTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGATTTGACGGCTGACGCTGCGGA  >  NC_000913/593843‑594133
                                                                                                                                                      |                                                                                                                                             
gcgTCAGCTCTTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGt                                                                                                                                               <  1:213917/151‑1 (MQ=255)
 cgTCAGCTCTTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTa                                                                                                                                              <  2:759108/151‑1 (MQ=255)
    cAGCTCTTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGaaa                                                                                                                                            >  1:633632/1‑150 (MQ=255)
         ctTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACa                                                                                                                                        <  1:744649/149‑1 (MQ=255)
            cGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTc                                                                                                                                   <  2:354739/151‑1 (MQ=255)
                  tagagtagagCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTaa                                                                                                                                             <  2:444357/135‑1 (MQ=255)
                  tagagtagagCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGaaaaaacgg                                                                                                                                      >  1:444401/1‑136 (MQ=255)
                        agagCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGAt                                                                                                                       <  1:619969/151‑1 (MQ=255)
                           gCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCat                                                                                                                    <  2:170285/151‑1 (MQ=255)
                           gCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAAACCTccaaacaccccatc                                                                                                                      >  1:370072/1‑136 (MQ=255)
                                 cTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGGAAGAAAACCTCAATACGCCCGGTCa                                                                                                                     >  2:139398/1‑144 (MQ=255)
                                   tCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTg                                                                                                             <  1:62448/150‑1 (MQ=255)
                                        cTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGGAAGAAATCCTCAATACGCTTGATCCTAttgttgtaag                                                                                                         >  2:667727/1‑145 (MQ=255)
                                         tCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGTAAGAAATCCTCAATAAACCCGCTCatat                                                                                                                  >  2:591112/1‑139 (MQ=255)
                                          ccTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACa                                                                                                      <  2:750611/150‑1 (MQ=255)
                                              cTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAACAACCTCAATAAACCCGATCATATGGGTGTAAGACAGt                                                                                                    >  1:900310/1‑148 (MQ=255)
                                               tGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAAAACTCAATAAGCTCCGTCATATTGTTGAAAGaaaagaac                                                                                                 >  1:95038/1‑143 (MQ=255)
                                                      gcgACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAATACCCAATAAACCCGATCATATGGGTGAAAAACAAAACCAGCT‑Gttt                                                                                        >  1:24735/1‑150 (MQ=255)
                                                        gACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCa                                                                                      <  1:196705/151‑1 (MQ=255)
                                                           tGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAATACTCCATACCCTCGCTCCTTTGGGTGGAAGAAAGTAACAACT‑GGTcccac                                                                                    >  2:613966/1‑147 (MQ=255)
                                                                gAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATg                                                                              <  2:525278/151‑1 (MQ=255)
                                                                    gCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAGAAATCCTCAATACACTCGATCATATGGTTGAAAGAAAGAACCAGCT‑GTTTCCGCCCaaatgg                                                                            >  1:701636/1‑145 (MQ=255)
                                                                               ttGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAAACCTCCATACCCTCCACCATATTGTTTTAAGACAGTAAAAACT‑GTTTCAGCCCCAACGGCACCGGCTTCggg                                                               >  2:278231/1‑151 (MQ=255)
                                                                               ttGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAAACCTCAATAAACTCGCTCATATGGTTGAAAGAAAGAAACAGCC‑GTTTCAACCCCAATGGCACGGGCTGCggg                                                               >  2:799895/1‑151 (MQ=255)
                                                                                        gagaTTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAACATCCTCAATACACCCGATCATATGGTTGAAAAACAATACCCGCTGGTTCCA‑CTCAATGGGCACGGGCTGCggggggggggg                                                       >  1:411253/1‑142 (MQ=255)
                                                                                                  aTTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAAAAAACCCCAATACACTCGATCATATGGTTGGAAGAAAGAACCAGCC‑GTTTCCCCTCCACGGGGACCGGCTGGGGGGGGGGGCGGACGGCga                                               >  2:915074/1‑148 (MQ=255)
                                                                                                   ttGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGGAAAGACATCCTCACTACGCTCGCTCCTATGGTTGGATGAGAGTACCAACG‑GTTTCACCCCAATGGGGACGGGCTGCGGGGCGGGGCGGACGTCggggt                                            >  1:248058/1‑146 (MQ=255)
                                                                                                      gtgtGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCttt                                        <  2:215016/151‑1 (MQ=255)
                                                                                                                 ttgTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAata                              <  2:469158/148‑1 (MQ=255)
                                                                                                                      aGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTgg                        <  1:625177/151‑1 (MQ=255)
                                                                                                                         gATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGAtt                     <  1:29360/151‑1 (MQ=255)
                                                                                                                            atCCGCTGAGAAATTGGACTGGCGGGGGAAAAAATCCCCCATAAGCTCCATTATAAGGGTGAAAAACAAAAACCGCA‑GTTTCAGCTCCATGGGGCCGGGCTGCGGGGCGGGGGGAACGCCGGGAACTTTTGCGGGAAtttttttggttt                    >  1:565045/1‑141 (MQ=255)
                                                                                                                              ccGCTGAGAAATTGGACTGGCGGGGAAAGAAATCCTCCATACGCCCGGTCATATGGTTGAACGGAAGAACCAGCC‑GTTCCCCCTCCAAGGGGACGGGCTGCGGGGCGGGGGGGACGGCGGGAACTTTTGCGGGGATATTTTGGGttttttg                >  2:447462/1‑147 (MQ=255)
                                                                                                                                     gaAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGATTTGACGGCTGACg         <  2:350436/151‑1 (MQ=255)
                                                                                                                                     gaAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGATTTGACGGCTGACg         <  2:85360/151‑1 (MQ=255)
                                                                                                                                              cTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGATTTGACGGCTGACGCTGCGGa  >  2:572671/1‑149 (MQ=255)
                                                                                                                                                      |                                                                                                                                             
GCGTCAGCTCTTCGAGATTAGAGTAGAGCACATCTTCCAGCTCCTTCTGGCTGCGCGACTGGCTGAGGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCT‑GTTCCAGCTCAATGGGCACGGTCTGCGGGTCGAGGCGAACGTCGAGATCTTTCGAGGTAATATTCTGGATTTGACGGCTGACGCTGCGGA  >  NC_000913/593843‑594133

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑