Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8800TC56.1% 32.8 / 55.5 41K271E (AAA→GAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (13/5);  new base C (0/23);  total (13/28)
Fisher's exact test for biased strand distribution p-value = 4.86e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.50e-08

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357731‑358015
                                                                                                                                                     |                                                                                                                                        
cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                         >  1:182952/1‑151 (MQ=255)
   gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                      >  2:760505/1‑151 (MQ=255)
        ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑a                                                                                                                                 >  2:940721/1‑150 (MQ=255)
          tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                               >  2:928073/1‑150 (MQ=255)
           gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aaca                                                                                                                              <  1:824979/150‑1 (MQ=255)
           gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                               <  1:345863/149‑1 (MQ=255)
              aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                          <  1:18606/151‑1 (MQ=255)
               aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                         <  2:244464/151‑1 (MQ=255)
                gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCCGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                         >  1:942168/1‑150 (MQ=255)
                  gTAGCGCATCAGGCAATTCCTGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgcc                                                                                                                      >  1:889348/1‑151 (MQ=255)
                   tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                     >  2:55688/1‑151 (MQ=255)
                                aaTTCCAGCCGCAGAGCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAACGCCGTTCTCTCCagt                                                                                                          >  1:119241/1‑149 (MQ=255)
                                   tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                     >  1:833336/1‑151 (MQ=255)
                                    ccAGCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTTTCTCCCAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                      <  2:12790/149‑1 (MQ=21)
                                      aGCCGCAGACCTGTGTCAGCGGCTACTGTGGTTCATTTCCGCCAACAACCGCGCATTTATCAAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGGCGC‑AACAAAACCGCCGTGCTCTCGAGTAGTGGCgg                                                                                                  >  1:808498/1‑151 (MQ=21)
                                       gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  >  1:475324/1‑150 (MQ=255)
                                              cccTGTGCCGGCGCCTACCGTGTTTCATTCCCCCCAACACCCGCCCTTTTATCCACCCCCATGTGCAAAAATCCCTCCGCGGCGGCTCTCTCCCATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                          <  1:427372/150‑1 (MQ=255)
                                                   tgccagggacTACGGTGATACTTTCCCGCAAAAACCCGCGCTTTTATCCAACGGCATGTCCAAAATTGCCTTCGGGGCGGCTGTCCGCCGGTTATTTTCCCGCCGA‑AACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                      <  2:363467/141‑1 (MQ=255)
                                                        gcgcCTACGGTGATTCTTTCCCGCCAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATGCTTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                <  2:584613/151‑1 (MQ=255)
                                                          gtcTACCGTGATTCTTTCCCCCCAACACCCGCGCATTTACCCAACGCCTTGTGCAAAAATCCCTTCGCGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                       <  2:713037/140‑1 (MQ=255)
                                                           cctcccttaaTTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCCATGTGAAAAAATCCCTCCGCGGCGCCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                <  1:726809/139‑1 (MQ=255)
                                                            cTACGGTTATTCTTTCCCACAAACACCCGCACTTTTACCAAACCCCTGGTAAAAAAATCCTTCCGCGGCGGTTGTCGCCCAGTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                             <  1:850144/150‑1 (MQ=255)
                                                             tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaaattttaaac                                                                           >  2:963721/1‑139 (MQ=25)
                                                               ccgttttcaaTTCCCCCCACCACCCGCACATTTACCCACCGCAATGTCCAAAATTCCCTCCGCGGCGGCTTTCTCCCAGCTATTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                             <  2:470988/138‑1 (MQ=255)
                                                                               ccAACACCCGCGCTTTTACCCACCGCCTTGTACAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                          <  2:891928/150‑1 (MQ=255)
                                                                                      ccGCGCTTTTACCCACCCCCGTTGCCAAAAAGGCTTGCGCGGGGGCTTCCTCCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCATCATGTTGTGTGGCAATc                                                       <  1:749897/146‑1 (MQ=255)
                                                                                       cgcgCATTTACCCACCGCCATGTGCAAAAAGGCCTCCGCGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                 <  2:343914/151‑1 (MQ=255)
                                                                                        gcgcTTTTACCCACCGCAATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCGGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                <  2:736152/151‑1 (MQ=255)
                                                                                         cgcTTTTACCCAACGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                <  2:430683/150‑1 (MQ=255)
                                                                                                  ccacccccATGTGAAAAAATCCCTCCGCGGCGGCTGTCGGCAAGTTATTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                        <  2:973080/143‑1 (MQ=255)
                                                                                                    accGCCATGTCAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                     <  2:252399/148‑1 (MQ=255)
                                                                                                                aaaaaTGCTTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                        <  2:554164/151‑1 (MQ=255)
                                                                                                                 aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCCTCCTGTTGTTTGGGGATCGCCGCTGGTAAAAATATGGGAAGGGGAggggg                       >  2:1002766/1‑147 (MQ=255)
                                                                                                                  aaaTGCCTCCGCGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                      <  2:593834/151‑1 (MQ=255)
                                                                                                                  aaaGGCTTTCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                      <  2:102866/151‑1 (MQ=255)
                                                                                                                   aaTGCCTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                     <  2:132330/151‑1 (MQ=255)
                                                                                                                              gggggcTGTCTCCAATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt            <  1:835340/146‑1 (MQ=255)
                                                                                                                              ggcggtTGTCTCCCGGCTTTTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc             <  2:455541/148‑1 (MQ=255)
                                                                                                                              ggcggcTGTCTGCCGGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc          <  2:980493/151‑1 (MQ=255)
                                                                                                                                        tccaacctttttttCCGCCAC‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAGCcg   <  2:826653/139‑1 (MQ=255)
                                                                                                                                          ccAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg   <  1:934882/146‑1 (MQ=255)
                                                                                                                                           cAGTTATTTTCCCGCCGC‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc    <  2:511472/144‑1 (MQ=255)
                                                                                                                                                ttttttCCCGCGCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc  <  1:615667/141‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                        
CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357731‑358015

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: ‑