Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA52.5% 5.3 / 44.9 40L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/6);  new base A (0/21);  total (13/27)
Fisher's exact test for biased strand distribution p-value = 2.25e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-04

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357742‑358035
                                                                                                                                                      |                                                                                                                                                    
gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caacaa                                                                                                                                                    <  1:766404/151‑1 (MQ=255)
 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTCTCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caaca                                                                                                                                                     <  1:899015/149‑1 (MQ=255)
   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                                                  <  2:661385/150‑1 (MQ=255)
   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                                                  >  1:746245/1‑150 (MQ=255)
          gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGtt                                                                                                                                        >  2:4199/1‑151 (MQ=255)
            gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTtct                                                                                                                                      >  2:1030859/1‑151 (MQ=255)
                  ggCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTCTCCAACGCCATGTGCAAAAATGCC‑TTCGCAGCGGCTGTCTGCCAGCTGTTTTTTCGGCC‑CAACACAA‑‑cgtgcactccttcc                                                                                                                                  >  1:104421/1‑136 (MQ=11)
                       tcccAGCCCAAGCCCGGTGTCAGCGCCTCCCGTGTTTCATTCCCCCCACCACCCGCCCATTTACCCAACGCCATGTGAAAAAAGGCC‑TTCGCGGCGGCTGTCTGCCATTTATTTTCCCCCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCagtagt                                                                                                                            <  2:889085/148‑1 (MQ=255)
                            gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                     >  2:262727/1‑151 (MQ=255)
                                ccgACCAGTGTCAGCGGCTACCGGGATTCATTTCCGCCAAAAAACGCGCATTTATCCAACGCCATGTGCAAAAACGCC‑TTCGCGTCGGATTTCTCCTAGCTTTTCTTCCGCCC‑CAACCAAA‑‑CCCCCGTTCTCTCCAGTAGTTGC‑g                                                                                                                       >  1:752381/3‑145 (MQ=255)
                                 agcttgtggccAGGGGCTGCCGTGATTCTTCCCCGCAACCACCCGCGCTTTCACCCACCGCGTGGTGAAAAATGGCC‑TCGGGGGGGGCTGTGTGCCGGTTTTTTTCCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                    <  1:505485/137‑1 (MQ=255)
                                   aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑ggggg                                                                                                                   >  2:611231/1‑145 (MQ=255)
                                    ccTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATGCT‑TTCGCGGGGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAagag                                                                                                              <  2:758206/150‑1 (MQ=255)
                                                gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaaaaaacatt                                                                                                    >  2:1088995/1‑141 (MQ=255)
                                                   aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAGGAGgaaaaacagttaaacc                                                                                              >  1:89250/1‑138 (MQ=25)
                                                    ccGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGGGAAAAAATGCC‑TCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCttt                                                                                                    <  1:218585/144‑1 (MQ=255)
                                                          ttattccccGCCACCACCCGCGTATTTCCCCAACGCCTTGTGAAAAAAGGCG‑TCCGGGGGGGCTGTGT‑CCCGTTTTTTTTCCCCCGAAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGc                                                                                                       <  1:867816/128‑1 (MQ=255)
                                                          ttCATTCCCCCCAACACCCGCGCATTTACCCACCCCCATGTGAAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCG‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                                          <  2:164891/148‑1 (MQ=255)
                                                                      aacaccCGCGCTTTTACCCACCCCCATGGGAAAAATTGCT‑TCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                           <  2:480989/151‑1 (MQ=255)
                                                                         acccccgcATTTACCCACCGCAATTGGAAAAACTCCC‑TTCGCGCCGGTTGTCTGCCACCTTTTTCCCCCCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                           <  2:689820/143‑1 (MQ=255)
                                                                           ccGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAGAGAAA‑AACATTAAAACCCTCATTTTTTGTgg                                                                                >  2:159949/1‑141 (MQ=25)
                                                                           ccGCCCATTTATCCACCGCCATGTGAAAAAATCCC‑TTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                      <  2:304672/151‑1 (MQ=255)
                                                                                       cccacccacgtggaaaaaaGGCCGTTGGCGGCGCTTGTCTGCCATGTTTTTTCCCGCCG‑‑AACAAAAT‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                     <  1:4198/127‑1 (MQ=255)
                                                                                           ccccATGTAAAAAAATGCC‑TGCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                       <  2:597492/148‑1 (MQ=255)
                                                                                              cATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAATTTTAAACCGCCCCGTTTTGTGGGGATCGCTGCTGGGTACAATGTggg                                                       >  2:752614/1‑146 (MQ=25)
                                                                                                tgtgAAAAAATGCT‑TTCGCGGCGGTTTTCTGCCAGTTTTTTTCCCGCCG‑CAACAAAC‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                                  <  2:666204/150‑1 (MQ=255)
                                                                                                tgtgAAAAAATGCC‑TTCGCGGGGGCTTTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                   <  2:104464/149‑1 (MQ=255)
                                                                                                    aaaaaaTGCC‑TCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCG‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                             <  2:894436/150‑1 (MQ=255)
                                                                                                     aaaaaTGCC‑TGCGCGGCGCGTGTCTCCAAGTTTTTTTCCCCCCA‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                              <  1:13699/149‑1 (MQ=255)
                                                                                                      aaaaccgcctcgggggcgtcTGTCGCCCAGTTTTTTTCCCCCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                            <  1:473860/137‑1 (MQ=255)
                                                                                                            gctgtcggggggcatGTCGGCCACTTTTTTTCCCGCCC‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                          <  2:517944/133‑1 (MQ=255)
                                                                                                            cc‑TGCGGGGCGGCTTTCTGCCATTTTTTTTCCCCCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                       <  2:534251/149‑1 (MQ=255)
                                                                                                                       ggttgtcggcggtttATTTTCCCGCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                                 <  1:816153/131‑1 (MQ=255)
                                                                                                                          tGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGGGAAAAAACATTTAACCCCCCCTGTTTTGTGGGGATCGCTGCTGGGTAAAAAGTGGGAAGGGGAGGGGGGGGGAACAGCCCCaca                           >  2:154091/1‑146 (MQ=255)
                                                                                                                                caagttATTTTCCCGCCG‑AAACAAAC‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                      <  1:966194/142‑1 (MQ=255)
                                                                                                                                       tttttCCGCCC‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg            <  2:898779/150‑1 (MQ=255)
                                                                                                                                       tttttCCCCCC‑CAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                               <  1:791160/133‑1 (MQ=255)
                                                                                                                                       ttttcCCGCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg              <  2:415270/148‑1 (MQ=255)
                                                                                                                                        ttttCCCCCA‑CAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGGAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa             <  2:874905/149‑1 (MQ=255)
                                                                                                                                         tttCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAAATTTTAAACCGTCCTGTTGTGTGGGGAACCCCGCTGGGGACAAAGTGGGAAGGGGAGGGGGGGGGAACAACTCCAAAAACGCCCCAAt                >  2:773204/1‑144 (MQ=255)
                                                                                                                                            ccgccg‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg        <  2:1131530/149‑1 (MQ=255)
                                                                                                                                            ccgcca‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc         <  1:798289/148‑1 (MQ=255)
                                                                                                                                                   caacaaAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAGATTTAAGCCCGTCCTGTTGTGTGGGGAAAGCTGCTGGGTAAAAAGTGGGAAGGGGAGGGGGGGGGATCAACCCCCCAAACCCGCCAATTTAGTTTTCCTcca  >  2:259043/1‑147 (MQ=255)
                                                                                                                                                   caacaaAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAACTTTTAACCCGTCCTTTTTTGTGGGAATCGCTGCTGGGGAAAATGTGGGAAGGGGAGGGGGGGGGATCAACTCCCCAACCCCGCTaa                 >  2:999813/1‑134 (MQ=255)
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GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357742‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑