Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	47.1%	57.8 / 14.9	51	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (22/5);  new base C (0/24);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 8.69e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357739‑358023                                                                                                                                                |                                                                                                                                                 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                                                                                                                              <  2:324163/151‑1 (MQ=255)           gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgcc                                                                                                                              <  2:345420/151‑1 (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)                                                                                                                                          ttttttcCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  2:911380/148‑1 (MQ=255)                                                                                                                                          ttttttcCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg           <  2:1153709/139‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                 CCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357739‑358023

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: ‑