Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	45.5%	27.8 / 26.5	44	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/8);  new base A (0/20);  total (16/28)
Fisher's exact test for biased strand distribution p-value = 2.67e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357741‑358034                                                                                                                                                       |                                                                                                                                                      tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                       >  2:765348/1‑150 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                                    >  1:536251/1‑149 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                                 <  2:826726/151‑1 (MQ=255)       gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                                                >  1:692030/1‑151 (MQ=255)         gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                              >  2:580030/1‑151 (MQ=255)              gcttCAGACAATTCCGGCCGCAATCTTGTGTCGGCGCCTACCGTCATCAATTCCCCCCAACACCCGCCTATTTATCCATCGCCATGTGCAAAAATCCCTTCGCGGCGCCTTTCTGCCAGTTATTTTT‑CCGCCGCAACAAAACCGCCGTtc                                                                                                                                          <  1:530335/147‑1 (MQ=255)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtct                                                                                                                                         >  2:815952/1‑151 (MQ=255)               cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                                                        >  1:846472/1‑151 (MQ=255)                              gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                        >  2:1032463/1‑151 (MQ=255)                              gCCGCAGACCTGTGTCAGCGGCTAACGTGATTCATTTCCGCCAACACCCGCGCATTTATCCAACGCCCTGTGCAACAATGCCTTCCAGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGAAACAAAACCGCCGCTCTCGCCAGTAGTGGC‑gg                                                                                                                         >  1:910073/1‑150 (MQ=255)                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                       >  2:86696/1‑150 (MQ=255)                                 gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                       >  2:82249/1‑149 (MQ=255)                                     acgtgtgTCGGGGGCTCCCGGTTTTCATTCCCCCCAACACCCGCTCTTTTACCCAACGCCATGTGAAAAACTCCCTCCGCGGGGGCTGTCTGCCGTTTTTTTTC‑CCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑Aag                                                                                                                  <  1:1117236/146‑1 (MQ=255)                                      ccggtgtCCGCGGCCCCCGTGTTTCTTTCCCCCCACCGCCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTCCGCGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑Aagag                                                                                                                <  2:411598/147‑1 (MQ=21)                                      ccTGGGTCAGCGGCTACCGTGATTCATTCCCCCCAACAACCGCGCATTTACCCAACGCCATGTGAAAAAATGCCTTCGGGGCGGTTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAgag‑a                                                                                                              <  2:977184/151‑1 (MQ=21)                                        tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggggca                                                                                                                    >  2:361362/1‑142 (MQ=255)                                             cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGACATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAagag                                                                                                                >  1:543657/1‑144 (MQ=255)                                              aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggggggcgagaga                                                                                                              >  1:583373/1‑136 (MQ=255)                                                 ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggggcggaggaaaa                                                                                                            >  2:960395/1‑133 (MQ=255)                                                     aCCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCACCCCCATGTAAAAAAATCCCTCCGGGGGGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGcc                                                                                                <  2:1139742/150‑1 (MQ=25)                                                            ttattccccGCCAACACCCCCGCTTTTCCCCAACCCTATGTAAAAAAATGCCTCCGCGGCGGCGTTCGGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  2:630866/143‑1 (MQ=255)                                                            tccttccccGCCACCACCCGGTCTTTTACCCAACCCCATGGAAAAAAACGCCTGCGCGG‑GGCTGGTCGCCGGTTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  1:804868/143‑1 (MQ=255)                                                                ttccccccAACACCCGCGCTTTTACCCACCGCCTTGTCCAAAAATGCCTTCGCGGCGGCTTCCTGCCAGTTTTTTTC‑CCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                       <  2:277156/142‑1 (MQ=255)                                                                ttcccGCCACCACCCGGGCTTTTACCAAACCCCATTTAAAAAAAGGCCTTCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCa                                                                                           <  2:783733/141‑1 (MQ=255)                                                                ttcccGCAAACACCCGCATATTTTCCCACCCCCATGTGAAAAAATGCTTCCGGGGCGGTTTTC‑GGCAGCTTTTTTTCCCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  2:631417/143‑1 (MQ=255)                                                                   cccccaccaACCCCGCTTTTACCCAACGCCAGGTGAAAAAACCCCTCGGCGCGGCCTGTCTGCCAGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                                   <  1:384164/146‑1 (MQ=255)                                                                        aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGG‑TAGAG‑GAAAAACTTTaaatccgccccgtt                                                                                       >  2:533164/1‑128 (MQ=25)                                                                           acccGCGCATTAACCCACCGCCAGGTGAAAAAAGGCCTCGGCGGCGGCTTTCTCCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                             <  2:546376/145‑1 (MQ=255)                                                                           acccGCGATTTTACCAAACGCCATGTGAAAAAATGCCTCCGCGGCGCCTTTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                         <  2:526921/149‑1 (MQ=255)                                                                              cgcgCTTTTCCCCAACGCAATGTGCAAAAATCCCTCCGCGGCGGCTTTCTGCCAGCTATTTTC‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct‑gct                                                                     <  1:281509/151‑1 (MQ=255)                                                                                cgcATTTACCCGACGCCGGGTGAAAAGACACCGTCGCGGCGGCTGTCGGCCAGCTTTTTTC‑CCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTgg                                                                   <  1:45302/151‑1 (MQ=255)                                                                                         ccACCGCCTTGTGAAAAAAGGCTTTCGGGGCGGCTTTCTCCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAAtgt                                                         <  2:583673/151‑1 (MQ=255)                                                                                         ccAACGCCATGTGCAAAAGTGCCTTCGCGGCGCCTGTCTGCCCGCTTTTTTT‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACaa                                                            <  2:536544/148‑1 (MQ=255)                                                                                         ccAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAAt                                                           <  2:387238/149‑1 (MQ=255)                                                                                         ccAACCCCATGTGAAAAAGCGCCTCCGCGGCGGCTGTCTCCCACTTATTTTC‑CCCCCGGAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAAtgt                                                         <  2:293552/151‑1 (MQ=255)                                                                                             cGCCATGTGAAAAAATGCCTTGGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGa                                                      <  2:581061/150‑1 (MQ=255)                                                                                                       aaaaggtccgcggcggcgGGTGTCGGCCAGTTTTTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAg                                              <  1:765006/136‑1 (MQ=255)                                                                                                             gCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGG‑AAAGG‑AAAAAATTTTAAACCC‑TCATGTTGTGTTGCCAACGGTGGCCGGTGAAAAATG‑GGAAAGGGAAggagg                                          >  2:252375/1‑143 (MQ=255)                                                                                                              ccTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGG‑GAGAGAAAAAAAGTTTAAG‑CCGCCCTCTTTTGTGGTGATCCCC‑TCTGGG‑AACAATGTGGAAAGGGGAGTggggggga                                     >  2:1089477/1‑146 (MQ=255)                                                                                                                  cgcgGCGTCTGTCTGCAATTTTTTTCC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCa                                  <  1:816752/149‑1 (MQ=255)                                                                                                                  cgcgGCGCCTGCCGCCCAGTTTTTTTC‑CCGCCACAACAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCa                                  <  1:578914/149‑1 (MQ=255)                                                                                                                   gcggcgCCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCa                                  <  2:1090710/148‑1 (MQ=255)                                                                                                                                      tATTTTT‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                  <  1:745514/145‑1 (MQ=255)                                                                                                                                              ccgccaAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc     <  1:798180/151‑1 (MQ=255)                                                                                                                                                 ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:240786/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                      TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357741‑358034

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: ‑