Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	42.9%	49.4 / 21.2	42	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (20/4);  new base A (0/18);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 2.12e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357742‑358022                                                                                                                                                      |                                                                                                                                       gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                                       <  2:203400/150‑1 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                                 >  1:771289/1‑151 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                >  2:665986/1‑151 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                               <  1:848310/151‑1 (MQ=255)          aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                             >  2:1025419/1‑151 (MQ=255)           tcgcatgatagcaTTCCAGCCGCAGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACGGCGATTTTCCCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                               <  2:210483/136‑1 (MQ=17)                 cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                      >  2:953324/1‑151 (MQ=255)                         tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                              >  1:503067/1‑151 (MQ=255)                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                             >  2:825156/1‑151 (MQ=255)                           cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                            >  1:314835/1‑151 (MQ=255)                              ccGCAGCCCGGGGCCGGCGCCTCCGGTTATTCTTTCCCCCCACCACCCGCGCTTTTACCCACCCCCTTGTGAAAAAAGGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         <  2:741232/151‑1 (MQ=255)                                gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                       >  1:237851/1‑149 (MQ=255)                                gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                        >  2:929521/1‑149 (MQ=255)                                 cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggt                                                                                                       >  2:116313/1‑148 (MQ=255)                                 cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         >  1:814757/1‑148 (MQ=255)                                       tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                       >  2:81960/1‑142 (MQ=255)                                         tgtCGGCGCCTCCCGTGTTTCTTTTCCCCAAACACCCGCCCTTTTACCCACCGCCATGTGAAAAAATGCTTCCGGGGCGGCTGTCTGCAAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag‑a                                                                                                   <  1:576321/145‑1 (MQ=255)                                          gccAGCGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCAATGTGAAAAAAGGCCTCCGCGGGGGTTGTCTGCCGGCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATa                                                                                             <  2:136948/148‑1 (MQ=255)                                                ggCTCCGGTGATTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTGCGCGGGGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                          <  1:88716/132‑1 (MQ=255)                                                ggCTACCGTTATTAATTCCCGCCACAACCCGCGCATTTATCCACCCCCATGTTAAAAAATGCTTTCGCGGGGGCTGTCTGCAAGCTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTaa                                                                                     <  1:168870/151‑1 (MQ=255)                                                ggCTACCGTGTTTCTTTCCCGCCACCACCCGCGCTTTTACCCACCGCATTGTACAAAAAGCCCTCCGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAAt                                                                                              <  2:60600/143‑1 (MQ=255)                                                  ccaCCGTATTTCATTCCCCCAACCACCCGCCCTTTTCCCCACCCCCTTGGGCAAAAATGCCTCCGCGGCGGCTGTCGGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑t                                                                                         <  2:467206/143‑1 (MQ=255)                                                  cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAG‑AGGAATaaaatt                                                                                        >  2:742305/1‑142 (MQ=255)                                                  cTACCGTGATTCATTCCCCCAAACACCCGCGATTTTACCCACCCCCATGTGAAAAAAGGCGTTCGGGGCGGCTGTCTGCCATCTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                            <  1:129918/128‑1 (MQ=255)                                                     ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAAGAAAAAAC‑TTTagacc                                                                                  >  2:567756/1‑146 (MQ=25)                                                          aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAG‑AGaaaaaaaatttaaacc                                                                                  >  1:729594/1‑132 (MQ=25)                                                             cATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGAAAAAAA‑TTTaaaaccgccctttt                                                                         >  1:63948/1‑138 (MQ=25)                                                              aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGGAAAAAC‑ATTTAACCCCTCCtgtt                                                                         >  2:75702/1‑149 (MQ=25)                                                                ttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑GGGAAAAGCATTTAATCCCgcctggtgt                                                                        >  1:999343/1‑141 (MQ=25)                                                                  ccGCAAACACCCGCGATTTTACCCAACGCCATGTAAAAAAATCCCTCGGGGGCGTCTGTCTGCAAGTTTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCAt                                                                            <  2:569751/142‑1 (MQ=255)                                                                     caaacaccCGCCCTTTTACCCACCGCCATGTAAAAAAAGCCCTGCGGGGGGCTTCTCTGCCATTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTtgtgtg                                                                    <  1:968768/145‑1 (MQ=255)                                                                                   tttACCCACCGCCATGTGAAAAAATCCCTGCGGGGCGGCTGTCT‑CCAGTTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                   <  2:1021638/150‑1 (MQ=255)                                                                                        ccacccccATGTGAAAAATTCCCTCCGGGGGGGCTGTCGCCCCTTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                 <  1:419334/141‑1 (MQ=255)                                                                                          acccccATGTGAAAAAATCCCTCCGCGGCGGCTTTCGGCAAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                            <  2:257518/146‑1 (MQ=255)                                                                                          aacccaagggaaaaaaaTCCCTCCGCGGCGGCTTTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                            <  2:775112/138‑1 (MQ=255)                                                                                           aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGAAAAAAA‑TTTTATACCCGCCTGTTTTGTGGCGATCGCTGCTGGTTACa                                                 >  1:71826/1‑144 (MQ=25)                                                                                             cccattgaaaaaaaGCCCTCCGCGGCCGTTCTCTGCCACTTCTTTTC‑CCGCCCCACAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                         <  2:630118/141‑1 (MQ=255)                                                                                              ccATGTGAAAAAACTCTTTCGCGGGGTCTTTCTCCCACTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                       <  2:608457/151‑1 (MQ=255)                                                                                                  ggcaaaaaaTGCCTCCGCGGCGGCTGTCGGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                          <  2:874199/140‑1 (MQ=255)                                                                                                                  gcggcgGTTTTGGGCCAGTTTTTTTC‑CCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                      <  2:1040239/148‑1 (MQ=255)                                                                                                                       ggcTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑GGAAAAAAA‑TTTAAAACCGCCATTTTTTGTGGGGATCGCCGCTGGGGACAAAGTGGGGAGGGGAGTgggggggggaaaatcc                 >  2:877732/1‑136 (MQ=255)                                                                                                                                ccAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt      <  1:81964/150‑1 (MQ=255)                                                                                                                                     ttttttc‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt  <  2:237839/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                       GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357742‑358022

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: ‑