Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	42.5%	62.5 / 10.1	47	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (18/9);  new base C (0/20);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 1.40e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCT  >  NC_000913/357735‑358018                                                                                                                                                  |                                                                                                                                                 tAGGCCTGATAAGCGTAGCGCGTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccg                                                                                                                                              <  2:236124/149‑1 (MQ=255) tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATACCTTCGCGGCGGCTGTCTGCCAGCTAGTTTT‑ccgcc                                                                                                                                            >  1:1064100/1‑151 (MQ=255)   ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgccg                                                                                                                                           <  1:378305/150‑1 (MQ=255)   ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑Ccgccgc                                                                                                                                          <  2:794452/151‑1 (MQ=255)       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)                                                                                                                                                  |                                                                                                                                                 TAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCT‑GCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCT  >  NC_000913/357735‑358018

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: ‑