Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA50.0% 38.4 / 31.6 48L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/8);  new base A (0/24);  total (16/32)
Fisher's exact test for biased strand distribution p-value = 6.52e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGC  >  NC_000913/357741‑358030
                                                                                                                                                         |                                                                                                                                               
tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                                 >  1:518230/1‑150 (MQ=255)
  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCCGCCCTGTGCCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaa                                                                                                                                              <  1:277835/151‑1 (MQ=255)
    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaaa                                                                                                                                             <  2:17119/150‑1 (MQ=255)
    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                            >  1:123078/1‑151 (MQ=255)
            cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtc                                                                                                                                    >  2:1051340/1‑151 (MQ=255)
               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtctc                                                                                                                                  >  2:911628/1‑150 (MQ=255)
                  aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                               >  1:1062720/1‑150 (MQ=255)
                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                      >  1:358491/1‑151 (MQ=255)
                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                      >  1:66079/1‑151 (MQ=255)
                                  agccttgtgTCAGCGGCTCCCGTGATTCATTCCCGCCAA‑CACCCGCGCTTTTAACAAACCCTTTGTGAAAAAAT‑GCTTT‑CGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCAA‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGG‑Caa                                                                                                              <  2:1081186/145‑1 (MQ=255)
                                   gACCTGTGCCAGCGCCTCCCGTGATTCATTCCCGCAAA‑CACCCGCGCATTTACCCACCGCAAGGTGAAAAAAG‑GCCTC‑CGGGGCGGCTGTCCGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑Ca                                                                                                               <  2:26073/148‑1 (MQ=255)
                                    acttttgtCAGCGCCTCCCGTGTTTCTTTCCCCCCAA‑CACCCGCGCTTTTACCCACCGCCATGTGAAAAAAG‑GCTTC‑CGGGGCGGCTGTCTGCCATTTTTTTTTCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  <  2:391629/140‑1 (MQ=255)
                                     ccTGTGTCAGCGGCTACCGTGATTCTTTCCCCCCAA‑CACCCGCGCATTTACCCACCCCCTTGTAAAAAAAT‑CCCTC‑CGGGGCGGCTGTCTCCCACCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAga‑g‑a                                                                                                        <  2:268722/151‑1 (MQ=21)
                                      cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggagggt                                                                                                               >  1:997022/1‑141 (MQ=255)
                                       tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑AAaga‑gga                                                                                                        >  2:309451/1‑148 (MQ=255)
                                          gtCGGCGGCTCCCGTAATTCTTCCCCCCAAA‑CACCCCCGATTTTACCCACCCCCATG‑GAAAAAAT‑TCCTTCCGGGGCGGCTGTCTCCCGGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑aa                                                                                                       <  1:469523/147‑1 (MQ=255)
                                            cggCGGCTCCCGTTATTCATCCCCGCCAA‑CCCCCGCGCTTTTCCCCACCGCCATG‑GAAAAAATGGCCTC‑CGCGGGGGCTGCCGCCCAGTTATTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAg                                                                                                   <  1:385346/147‑1 (MQ=255)
                                              gCGGCTACGGTAATTCTTTCCCGCAAA‑CACCCCCGTTTTAACCCAACCCCATGTCAAAAAAT‑GCCTT‑CGGGGCGGCTGTCGGCCTGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATa                                                                                                    <  2:939751/146‑1 (MQ=255)
                                                    aCCGTGATTCATTCCCCCCAA‑CACCCCCGCTTTAACCCACCGCGGGGTGAAAAAAT‑CCCTA‑GGCGGCGCTCGTCTGCCAGCTTTTTCCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTa                                                                                              <  2:505210/146‑1 (MQ=255)
                                                     ccGTAATTCTTTCCCCCAAA‑CACCCCCGCTTTTCCCCAACCCCATGTGAAAAAAG‑GCTTT‑GGCGGCGGCTGCCGGCAGGCTTTTTTCCCGCGGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCttt                                                                                               <  1:576002/144‑1 (MQ=255)
                                                         taattctttCCCCCAACCACCCCCGCTTTTACCCCCCGCCAGGTAAAAAAAC‑CCCTC‑CGGGGCGCTTGTC‑GCCCGTTTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGcc                                                                                          <  1:792276/140‑1 (MQ=255)
                                                           ttCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CGAGA‑G‑GAAAAAGTTTAAAccccccctct                                                                                  >  2:456940/1‑144 (MQ=25)
                                                             cATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggcgggagaggga                                                                                                         >  1:187500/1‑118 (MQ=255)
                                                               ttcccccaaa‑caccCGCCCTTTTACCCAACGCCATGGAAAAAAAT‑CCCTC‑CGCGGCGGTTGTCTCCCAGTTTTTTTCCCGCCAA‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCAt                                                                                    <  1:197719/137‑1 (MQ=255)
                                                                   cGCCAC‑CACCCGCGCTTTTAGCCAACGCGATTGGAAAAACG‑GCCTT‑CGCGGCGGCTGTCTCCCATTTATTTTCCCCCCCA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                 <  2:1047781/144‑1 (MQ=255)
                                                                     ccAA‑CACCCGCGCTTTTACCCACCCCCATGTGAAAAAAT‑GCCTC‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                         <  2:368693/150‑1 (MQ=255)
                                                                       aa‑caccCGCGCATTTACCCAACGCCTTGTGAAAAAAT‑GCCTT‑CGGGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                      <  2:209819/151‑1 (MQ=255)
                                                                             ccGCGTATTTACCCACCCCCTTGTAAAAAAGT‑CCCCC‑CGCGGCGGCTCCCTGCCAGTTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                   <  1:1051245/149‑1 (MQ=255)
                                                                                      tacccAACGCCATGTGCAAAATT‑GCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                         <  2:467886/147‑1 (MQ=255)
                                                                                         ccACCGCCAGGTGAAAAAAT‑CCCTT‑CGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                      <  2:501296/150‑1 (MQ=255)
                                                                                           acccccttgtgAAAAAAT‑GCCTT‑CGGGGCGGCTGTCTGCCAGTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                    <  2:781045/143‑1 (MQ=255)
                                                                                               ccATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGAGG‑AAAAAAATTTAA‑CCCCCCCTGTTTTGTGGGGATCGCTGCTggggaaaaaatgg                                                   >  1:1015016/1‑136 (MQ=21)
                                                                                                    tgCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGA‑G‑AAAAAAAGTTAAATCCGCCCAGTTTTGTGGGAAACGCCGTTGGGGACAATGAGGAAAggg                                             >  2:312261/1‑148 (MQ=255)
                                                                                                       aaaaaC‑GCCTC‑CGGGGGGGCTGTCGCCAATCTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                            <  1:500222/146‑1 (MQ=255)
                                                                                                          aaT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAACG‑G‑AAAAACGTTTAATCCC‑TCCCGTTGTGTGGGGAACGCTGCTTGTGACAATGTGGGAAGGGGAgagggg                                     >  2:625971/1‑145 (MQ=255)
                                                                                                            aacgctctggcggcgGCTGCCGGCCAGTTTTTTCCCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                    <  1:363883/142‑1 (MQ=255)
                                                                                                                  tcggcggggGCTGTCTCCCGGTTTTTTTCCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                 <  1:434163/145‑1 (MQ=255)
                                                                                                                     gggggggcTGCCGGCCATTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                              <  1:524112/143‑1 (MQ=255)
                                                                                                                       ggcggcTGTCTGCCATCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                              <  1:873583/146‑1 (MQ=255)
                                                                                                                           gcTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACAGCCGTTCTCTCCAGTAGTGGCGGGG‑CGAGA‑G‑AAAAAAATTTTAACCCCCCCTGTTTTGTGGGGATCGCTGCTGGTTACAAAATGGGAAGGGGAGGGGGGGGGATCaaatcc                         >  2:489899/1‑142 (MQ=255)
                                                                                                                                cTGCCGGCTTTTTTTCCGCCGA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                    <  1:994824/147‑1 (MQ=255)
                                                                                                                                 tgcaagtttttttcCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                   <  2:912005/122‑1 (MQ=255)
                                                                                                                                  gCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAAAAAACTTTAAACCC‑CCCTGTTGTGTGGGGAGTGCTTCTGGGAACAATGTGGGGAGGGGAGGGGGGGGGAGCAACTCCCAAAACgcgc               >  2:782822/1‑150 (MQ=255)
                                                                                                                                   ccAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                   <  1:728133/145‑1 (MQ=255)
                                                                                                                                     acttATTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa             <  2:384274/146‑1 (MQ=255)
                                                                                                                                         tttttcCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa            <  2:262791/145‑1 (MQ=255)
                                                                                                                                          tttttCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAAAAAAATTTAAACCC‑CCCTGTTGTTTGGGGATCCCCGCCGGGGACAAAGTGGGAAGGGGAGGGCGGGGGATCAGCTCCACAACCGCCCCAAtt          >  2:1003184/1‑147 (MQ=255)
                                                                                                                                           ttttCCGCCGA‑AACAAATCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt      <  2:76670/150‑1 (MQ=255)
                                                                                                                                              cccgcccC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGc  <  1:82650/150‑1 (MQ=255)
                                                                                                                                                         |                                                                                                                                               
TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGC  >  NC_000913/357741‑358030

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: ‑