Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.1%	31.8 / 77.7	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/9);  new base A (1/23);  total (15/32)
Fisher's exact test for biased strand distribution p-value = 2.85e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.36e-06

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357742‑358031                                                                                                                                                       |                                                                                                                                                 gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                                                 <  2:154163/150‑1 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                                                 <  2:767486/150‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                               <  1:560587/151‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑c                                                                                                                                            >  1:190807/1‑151 (MQ=255)     aGCTTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑cc                                                                                                                                           <  2:705425/151‑1 (MQ=255)      acGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑ccg                                                                                                                                          <  2:577612/150‑1 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑ccgcc                                                                                                                                        <  2:195273/151‑1 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑ccgcc                                                                                                                                        >  2:237747/1‑151 (MQ=255)          accgcATCCGCCAATCCCAGCCGCAGACCTT‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑ccgcc                                                                                                                                        <  1:870730/147‑1 (MQ=255)               aTCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTtctct                                                                                                                                 >  2:532878/1‑151 (MQ=255)                  aGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                               >  1:424413/1‑150 (MQ=255)                        tcccagccccag‑ccTGTTGTCGGCGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCTTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCagtagt                                                                                                                         <  2:801928/148‑1 (MQ=255)                        tcccAGCCGCAGCCCTG‑TGTCAGCGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCTTTTATCCAACGCCATGTACAAAAATCCCTTCGCGGCGGCTGTCTGCCAGCTATTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCagta                                                                                                                           <  2:29067/146‑1 (MQ=255)                                gCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  2:137622/1‑149 (MQ=255)                                   gACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  2:592261/1‑146 (MQ=255)                                       tg‑tgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggcagggga                                                                                                          >  2:239751/1‑142 (MQ=255)                                          tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑gaa                                                                                                        >  1:357403/1‑149 (MQ=255)                                           gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggcggaggaaaa                                                                                                       >  1:455590/1‑139 (MQ=255)                                                  gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaaaaaattt                                                                                                 >  2:866931/1‑141 (MQ=255)                                                   cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑aaaaaaact                                                                                                  >  2:577008/1‑140 (MQ=255)                                                     cccGTGATTCATTCCCCCCACCCCCCGCGCTTTTACCCACCCCCTGGTAAAAAAATGCCTCCGGGGGGGTTGCCGGCCGGTTTTTTTC‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGccc                                                                                           <  1:677040/150‑1 (MQ=255)                                                      ccGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATGCTTCCGGGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGccc                                                                                           <  2:644026/150‑1 (MQ=255)                                                                ttccccccAACACCCGCGCTTTTACCCAACCCCATGTGCAAAAATCCCTTCGCGCCGGCTGTCTGCCAGTTTTTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgt                                                                                    <  2:1000000/141‑1 (MQ=255)                                                                ttccccccAACACCCCCGCATTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                   <  2:455818/142‑1 (MQ=255)                                                                ttcccGCCAACACCCGCCCTTTTACCCACCCCAAGGGGAAAAAGGGCCGCGGGGGGGGCGGTCTGCCGGTTATTTGC‑CCGCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                   <  1:105964/145‑1 (MQ=255)                                                                   cccccAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTGCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                             <  2:152672/148‑1 (MQ=255)                                                                            ccgccgcATTTACCCACCGCCTTGTAAAAAAAGGCTTGCG‑GGGGGCTGTTCGGCAGGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                        <  1:282727/143‑1 (MQ=255)                                                                             ccGCTCATTTCCCCACCGCCTTGTACAAAAATCCCTTCGCGGCGGCTGTCGGCGAGCTTTTTTC‑CCGCGAAAAAAAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                     <  1:578512/149‑1 (MQ=255)                                                                                  cATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAG‑AAAAAACTTTTAAACCCCCCTGTTGTGTggggaacgc                                                                      >  2:943822/1‑136 (MQ=25)                                                                                            ccGCCATGTGCAAAAATGCCTTCGCGGGGGCTGCCTGCCAGCTATTTTC‑CCGCCGAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGa                                                   <  1:223730/150‑1 (MQ=255)                                                                                             ccccATGTGAAAAAATGCCTGCGCGGGGGTTGTCTGCCGGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGa                                                   <  1:698317/148‑1 (MQ=255)                                                                                             cGCCTTGTGCAAAAATCCCTCCGCGCGGGCGTCCGGCAAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGa                                                   <  1:1023837/150‑1 (MQ=255)                                                                                             cGCCTTGTAAAAAATTGCCTCCGGGGGGGCTGTCTCCCGTTTTTTTTC‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg‑tg                                                     <  1:520413/148‑1 (MQ=255)                                                                                             cGCCATTTGAAAAAATGCTTCCGCGGCGGCTGTCGGCCAGCTTTTTTT‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑Tgg                                                    <  2:79126/149‑1 (MQ=255)                                                                                                cATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAAATTTAAACCC‑CCATGTTTTGTGGGGAACGCTGCTggggaaaaagtgggaa                                                  >  2:709381/1‑135 (MQ=19)                                                                                                       aaaaaTGCCTCCGCGGCGGCTTTCTGCCAGCTTTTTTC‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTg                                         <  2:739270/150‑1 (MQ=255)                                                                                                       aaaaaTCCCTTCGCGGCGCCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGaa                                            <  2:1007857/147‑1 (MQ=255)                                                                                                              cctcggcggcgGCTGTCGGCCAGTTTTTTTC‑CCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGaa                                  <  1:379577/145‑1 (MQ=255)                                                                                                                    cggcggCTGTCTGCCAGCTATTTTT‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCTAGAC‑AAATAACTTTTATACACTCACGTTGTGTGTGTATGGCTGGTGCTAAAAATGATGGAAA‑GGAAGTgtggggcataaggt                            >  1:181233/1‑140 (MQ=255)                                                                                                                     ggcggcTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAAt                                 <  2:78268/144‑1 (MQ=255)                                                                                                                     gccggcTGTCGGCCGGTTATTTTT‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTgcggcg                                    <  1:436099/139‑1 (MQ=255)                                                                                                                                 ccATCTTTTTTC‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                  <  1:803751/147‑1 (MQ=255)                                                                                                                                  ccagttttttt‑CCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa              <  1:572961/145‑1 (MQ=255)                                                                                                                                   agtttttttc‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTcc                          <  1:223944/132‑1 (MQ=255)                                                                                                                                   agtttttttc‑CCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt               <  2:697049/143‑1 (MQ=255)                                                                                                                                      ttttttc‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCa                         <  1:596333/133‑1 (MQ=255)                                                                                                                                        ttttc‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg          <  2:932485/148‑1 (MQ=255)                                                                                                                                              ccgccgCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc     <  2:190914/148‑1 (MQ=255)                                                                                                                                               cgccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAAACCCCCCTGTTTTGTGGGGATAGCCGCTGGGGAAAATG‑TGGAAAGGGGAGGGGGGGGGAGAAGCTCCACAAACCCGCCAAATTAGGTCGcc  >  2:7825/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                                 GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTG‑TGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG‑TGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357742‑358031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑