Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	43.1%	65.7 / 22.2	53	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (23/6);  new base T (0/22);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 2.46e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357727‑358017                                                                                                                                                       |                                                                                                                                                tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                               >  2:806448/1‑151 (MQ=255)   aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                             <  2:1076380/151‑1 (MQ=255)             ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                                    >  1:1500275/1‑150 (MQ=255)                  tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGACTGTCTGCCAGCTATTTTTCCGCCGCAAC‑aaa                                                                                                                              >  1:1359069/1‑150 (MQ=255)                    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAcc                                                                                                                           <  2:158504/151‑1 (MQ=255)                       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgcc                                                                                                                        <  2:345420/151‑1 (MQ=255)                       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgcc                                                                                                                        <  2:324163/151‑1 (MQ=255)                         aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGt                                                                                                                      >  1:945795/1‑151 (MQ=255)                           cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTtc                                                                                                                    >  1:174578/1‑151 (MQ=255)                           cccATCAGGCAATCCCAGCCGCAGCCCTGTGTCAGCGCCTACCGTGATTCATTCCCGCCAACACCCGCGCATTCATCCACCGCCAGGTGAAAAAAGGCCTC‑C‑GCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGCAAC‑AAAAccgccg                                                                                                                       <  1:545339/146‑1 (MQ=17)                               ccgtactatcccAGCCGCAGCCCTGTGCCGCCGGCACCGGTGGTTCTTTCCCGCCAAAACCCGCGTTTTTGCCCACCGCCAGGTGAAAAAATGCTTT‑C‑GCGGCGGTTGTCGGCGATTTTTTTTCCCGCCGCAAC‑AAAACCGCCGTtctctc                                                                                                                <  1:240265/141‑1 (MQ=255)                                     aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCagt                                                                                                            >  1:163980/1‑149 (MQ=255)                                     aaTCCCACCCGCAGCCTTTTGCCAGGGCCTCCCTTGATTCTTTCCCCCCACCACCCCCGCTTTTACCAAACGCCATGTGAAAAAATGCCTT‑C‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCagt                                                                                                            <  2:1425961/149‑1 (MQ=255)                                         ccacccacAGACTTTTGTCGGCGGCTCCGGTTATTCTTTCCCGCAAACACCCCCGCTTTTACCCACCCCATTGTG‑AAAAATGGCTTGC‑GCGGGGTCTTTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCagta                                                                                                           <  2:902377/146‑1 (MQ=255)                                          cgcccgcgaccttgtgTAAGCGGCTCCCGTGTTTCATTCCCCCAACCACCCCCGCTTTTACCCACCCCCATGTAAAAAAATCCCTC‑C‑GCGGCGGCTGCCGGCCAGCTTTTTTCCCCCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                     <  2:132861/139‑1 (MQ=255)                                              cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGACGTTCTCTCCAGTAGTGGCggg                                                                                                   >  1:1420793/1‑149 (MQ=255)                                               gCAGACCTGTGACAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                    >  1:219328/1‑147 (MQ=255)                                                cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCggtg                                                                                                  >  2:363351/1‑146 (MQ=255)                                                cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                >  1:1321538/1‑148 (MQ=255)                                                 aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                 >  1:62728/1‑147 (MQ=255)                                                  gACCTGTGCCGGCGCCTCCCGTATTTCTTTCCCCCCAAAACCCGCCCTTTTCCCCACCCCCATTTAAAAAATTCCCTC‑G‑GCGGGGGCTGTCGGCCGGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                <  1:580955/148‑1 (MQ=255)                                                   ccttgtgTCGGCGCCTCCCTTATTTCTTTCCCCCCAACACCCGCCTTTTTACCCACCCCCTTGTGAAAAAATCCCTC‑C‑GGGGCGGCTTTCTCCAAGTTTTTTTCCCGCCACAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                              <  1:1080564/146‑1 (MQ=255)                                                      tgtgTCAGCGACTACCGAGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATCTGCAAAAATGCCTT‑C‑GCGGCGGCCGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGTGcc                                                                                                >  1:157554/1‑143 (MQ=255)                                                        tgtCGGCGCCTCCCGTGTTTCTTTCCCGCAAACACCCGCGCTTTTACCCACCCCCTTGTGAAAAAATCCCTC‑C‑GCGGCGGCTTTCTCCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                         <  2:286737/149‑1 (MQ=255)                                                            aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaa                                                                                      >  2:500210/1‑145 (MQ=255)                                                             gCGGCTACGGTTATTCTTTCCCCCAAACACCCGCGCTTTTACCCAACCCCTTGTAAAAAAATCCTTC‑C‑GGGGCGGCTTTCTCCCATTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                        <  2:1571975/145‑1 (MQ=255)                                                               gcctcccttatttCATTCCCCCAAACACCCGCGTTTTTACCCACCCCCATGTAAAAAAATCCCTC‑C‑GGGGCGGCTGTCTCCCAGTTTTTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                        <  2:1337094/132‑1 (MQ=255)                                                                   acatcgtttCATTCCCCCCAACCACCCCAATTTTCCCCACCCCCATGTAAAAAAATGTTTC‑C‑GGGGCGGCTGTCTTCCACTTCTTTTCCCCCCCCACA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                   <  2:156423/137‑1 (MQ=255)                                                                     cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcggggggcaaaa                                                                                      >  2:1082606/1‑128 (MQ=255)                                                                          ttcttccccGCAAACACCCGCGCTTTGCCCCACCGCCATGT‑AAAAAATTCCTT‑CGGCGGCGGTTGTCTGCCAGTTTTTTTCCCCCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                       <  1:1425269/142‑1 (MQ=255)                                                                          ttCTTTCCCACCAACACCCGCGCTTTCACCCACCCCAATGGAAAAAAAGGCTTC‑C‑GCGGCGGCTTCCTGCCATGTTTTTTCCCGCCACAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                       <  1:66957/149‑1 (MQ=255)                                                                              ttcccccaaacaccCGCGTTTTTATCCACCGCAATGTCAAAAAATCCTTT‑G‑GGGGGGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                         <  2:1448017/135‑1 (MQ=255)                                                                                ccccccAACACCCGCGTTTTTACCAACCCCCATGTGCAAAATGCCCTC‑C‑GCGGCGGCTTTCTGCCGGTTATTTTCCCGCAGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                               <  2:980333/147‑1 (MQ=255)                                                                                cccGCCAACACCCGCGCTTTCCCCCAACGCCTTGTGAAAAAAGCCTTT‑C‑GGGGCGGCTTTCGGCCGGTTTTTTTCCGGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                        <  1:233096/141‑1 (MQ=255)                                                                                 cccccAACACCCGCGCATTTATCCAACGCCATGTGAAAAAATGCCTC‑C‑GCGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                                 <  2:1025007/145‑1 (MQ=255)                                                                                 ccGCCAACATGGGCACATTTCCCAAACACCATGTGCAAAAACGCCTC‑C‑GCGGCCGTCGCCTGCCAGCT‑TTTTTCCCCCGCCACAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                       <  2:390182/142‑1 (MQ=255)                                                                                       acaccCGCGTTTTTCCCCAACCCGATGTGAAAAAGCCCCTC‑C‑GCGGCGGCTTTCTGCCAGCTTTTTTCCCGCGGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                          <  2:333236/149‑1 (MQ=255)                                                                                          acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAAATTTTATACCCGCCTGTTGTTTGGGAATTgctg                                                     >  2:1187174/1‑151 (MQ=21)                                                                                               gcATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTTAAACCCTCATCTTTTGTgggga                                                           >  2:606946/1‑137 (MQ=25)                                                                                                 aTTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGCAAAAACTTTTAACCCCCCCCGTTGTTTGGGAATCGCCGCCgg                                                 >  2:251574/1‑148 (MQ=25)                                                                                                        cAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCGCATGTTGTGTGGGAAACGGCGCTGGGAACaa                                           >  2:675516/1‑147 (MQ=37)                                                                                                         aaCGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTATACCCTCCTGTTTTTTGGGGATCGCTGCTGGGAACa                                            >  2:535050/1‑145 (MQ=25)                                                                                                            cccATGTGAAAAAATCCCTT‑C‑GCGGCGGCTGTCTGCCATTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                   <  2:414859/150‑1 (MQ=255)                                                                                                                  tgCAAAAATCCCTC‑C‑GGGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                               <  2:596314/149‑1 (MQ=255)                                                                                                                     aaaaaTGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAATTTTAAACCCTCCTGTTTTGTGGGGATAGCTGCTGGTGAAAAAATGGGAAggggggggg                          >  2:886000/1‑145 (MQ=255)                                                                                                                       aaaagatcctcctcggctgCTGTCTGCCTGCTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                            <  2:1144083/136‑1 (MQ=255)                                                                                                                                     ggggtcTGTCGCCCCGCTATTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc               <  2:837265/143‑1 (MQ=255)                                                                                                                                      gcgccTGCCTGCCATTTTTTTTCCCCCCACAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc            <  1:890037/150‑1 (MQ=255)                                                                                                                                          cTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAACTTTTATCCCGCCATGTTTTGTGGGAATCCCTGCTGGGTACAATGTGGGAAGGGGAGGGGGGCGGATCaaccccc           >  2:360066/1‑141 (MQ=255)                                                                                                                                           tGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAACTTTAAGACCCTCCTGTTGTGTGGGAATCGCTGCTGGTAACAAAGTGGGAAGGGAAGTGGGGCGAATCAGCCCCAGaa        >  1:732710/1‑149 (MQ=255)                                                                                                                                             tCTGCCATTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa           <  2:465013/144‑1 (MQ=255)                                                                                                                                             tCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGTGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc    >  2:785024/1‑151 (MQ=255)                                                                                                                                                 ccAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc  <  2:174599/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357727‑358017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑