Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA41.5% 32.4 / 22.9 41L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (18/6);  new base A (0/17);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 6.89e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033
                                                                                                                                                         |                                                                                                                                                
cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                  >  1:1212912/1‑151 (MQ=255)
  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                 <  1:351151/150‑1 (MQ=255)
   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                >  2:1227982/1‑150 (MQ=255)
   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                 >  2:80591/1‑149 (MQ=255)
    tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                               >  1:1227862/1‑150 (MQ=255)
     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                              <  2:614645/150‑1 (MQ=255)
       gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                           <  1:1077911/151‑1 (MQ=255)
       gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                            >  2:781766/1‑150 (MQ=255)
            gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                                                                                                                                      >  1:1219033/1‑151 (MQ=255)
                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑CACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                          >  2:321880/1‑149 (MQ=255)
                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                        >  1:174389/1‑151 (MQ=255)
                              gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                     >  1:35459/1‑150 (MQ=255)
                               ccGCACACCTTTTTCACCGGCTACCGTGTTTCTTTCCCCCC‑ACCACCCGCGTTTTAACCCACCCCCTT‑GTGAAAAAATGCTTT‑CGGGGCGGCGGCCTCCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                    <  1:655898/150‑1 (MQ=255)
                                          tgtCGGCGGCTACTGTCTTACATTCCCCCC‑AACAACCGCGCATTAACCCAACGCTAT‑GGCAAAAAATCCTTT‑CGCGGCGGCTGTCTGCCACCTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                         <  1:446821/150‑1 (MQ=255)
                                             cAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAATCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                      >  2:1164669/1‑134 (MQ=255)
                                               gcgcctccggtttttCTTTCCCCCC‑AACACCCGCCCTTTTACCCACCCCCAT‑GTAAAAAAATGCCTC‑CGCGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                         <  1:1075844/132‑1 (MQ=255)
                                                cGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTTTCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGAAAAAGAtt                                                                                                    >  1:1257533/1‑149 (MQ=21)
                                                cGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggacgggaaaga                                                                                                       >  1:1225869/1‑134 (MQ=255)
                                                  gcctcccgtatttctttCCCCCAAACACCCGCGTTTTTACCAACCGCATT‑GTAAAAAAATCCTTC‑CGGGGCGGCTGTCTCCCATTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                           <  1:718284/127‑1 (MQ=255)
                                                    tcccGTGTTTATTTCCCCCC‑ACCACCCCCGCTTTTTCCCACCGCCGT‑GTGAAAAAAGCCCTC‑CGCGGGGGCTGTCCCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                                    <  1:763065/143‑1 (MQ=255)
                                                    tACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGTAacaggcacaagagtta                                                                                                 >  2:470772/1‑136 (MQ=25)
                                                    tACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTA‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGaaaaaaaattttaccc                                                                                             >  2:594535/1‑138 (MQ=21)
                                                     aCCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaaattaaaacc                                                                                             >  1:352125/1‑138 (MQ=25)
                                                      ccgtattccATTCCCGCC‑ACCACCCCCTCTTTTCCCCAACGCCTT‑TGGAAAAAATCCTTC‑CGGGGCGGCTGTCTCCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                                <  1:321361/139‑1 (MQ=255)
                                                       cGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatttagccc                                                                                             >  2:717536/1‑136 (MQ=25)
                                                        gTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaaaaaaatttagaac                                                                                             >  1:600773/1‑135 (MQ=255)
                                                            ttCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGGGAAAAAGCcttttaaccgccctct                                                                                      >  1:969935/1‑138 (MQ=25)
                                                                 tcccccc‑AACACCCGCGCATTTACCCAACCCCAT‑GTCAAAAAATGCCTC‑CGCGGCGGCTGTCTCCCATCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                   <  1:959821/144‑1 (MQ=255)
                                                                  cccccc‑AACACCCCCGCTTTTACCCACCCCATT‑GTAAAAAACCGCCTC‑CGCGGCGGTTTTCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                                           <  2:650804/136‑1 (MQ=255)
                                                                   ccccc‑AACACCCGCTATTTAACCCAACCCTAT‑GTG‑AAAAATTCCTTGCGGGGCGGCTTTTTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                               <  1:696134/148‑1 (MQ=255)
                                                                    cccc‑AACACCCGCGC‑TTTTCCCCACCCCATGGTGAAAAAATGCCTC‑CGGGGGGCCTGTCTGCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                              <  2:744587/149‑1 (MQ=255)
                                                                                              acccaaggaaaaaaatTGCCTC‑CGCGGCGCTTTTCTCCTATCTTTTTTTCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtgt                                                        <  1:340584/137‑1 (MQ=255)
                                                                                                     gcaaaaaaaTGCGTC‑CGCGCCGCCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAg                                                  <  1:164594/143‑1 (MQ=255)
                                                                                                         aaaatTCCCTT‑CGGGGCGCTGGTCCCCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTg                                           <  1:727084/150‑1 (MQ=255)
                                                                                                         aaaaaCGCCTT‑CGGGGCGGCGCTCGCCCAATTATTTTTCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTgc                                          <  1:204567/151‑1 (MQ=255)
                                                                                                          aaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGACGAGAAATAGCATTAAAACCCTCATGTTGTTGGGGAAATGCTGCTGGTGACAAAACTGGAAAGGGaggggg                                          >  1:1079622/1‑146 (MQ=255)
                                                                                                                        ggcggtTGTCGACCATTTTTTTTCCCGCAGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGa                                     <  2:574725/142‑1 (MQ=255)
                                                                                                                        ggcggcTGTCCGCCGCTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGc                               <  1:1228046/148‑1 (MQ=255)
                                                                                                                                    cgaattATTTCCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                      <  2:798882/140‑1 (MQ=255)
                                                                                                                                         ttttttcCCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                    <  2:1074251/140‑1 (MQ=255)
                                                                                                                                           ttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg          <  2:62066/150‑1 (MQ=255)
                                                                                                                                            tttcCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt         <  1:594554/150‑1 (MQ=255)
                                                                                                                                                 cgccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACCCGTCATTTTGTGTGGGGATCGCCGCTGGGGAC‑AAAGTGGGAAGGGGAGGGGGGCGAATCAGCTCCCGAAACCCGCTAAATTAGttt       >  1:697771/1‑146 (MQ=255)
                                                                                                                                                 cgccacAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt   <  1:627233/151‑1 (MQ=255)
                                                                                                                                                    cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTTAACCCCCCATGTTGTGTGGGGAACGCTGCTGGGTAC‑AAAATGGGAAGGGGAGGGGGGGGGAACAACCCCCGAACCGCGCCAATTTAGTTTGCCTc  >  1:1272706/1‑149 (MQ=255)
                                                                                                                                                         |                                                                                                                                                
CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑