Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,332,791	0	A	C	42.9%	87.0 / 13.8	49	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
Reads supporting (aligned to +/- strand):  ref base A (26/2);  new base C (0/21);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 6.48e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGTTGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGG  >  NC_000913/4332642‑4332932                                                                                                                                                           |                                                                                                                                              cATGTTGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCAc                                                                                                                                              >  1:497625/1‑151 (MQ=255)  aTGTTGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCAcc                                                                                                                                             <  2:892552/151‑1 (MQ=255)      tGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCg                                                                                                                                         >  1:305546/1‑151 (MQ=255)         tAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGcc                                                                                                                                       >  1:480747/1‑150 (MQ=255)            ttACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCGGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTg                                                                                                                                   >  2:707110/1‑151 (MQ=255)            ttACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTg                                                                                                                                   >  1:754570/1‑151 (MQ=255)             tACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTgg                                                                                                                                  >  2:807042/1‑151 (MQ=255)               ccGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCg                                                                                                                                >  2:462642/1‑151 (MQ=255)                        aaTGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGtt                                                                                                                       >  1:700726/1‑151 (MQ=255)                         aTGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTc                                                                                                                      >  1:124471/1‑151 (MQ=255)                                tCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCATACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGcgcg                                                                                                               >  1:312947/1‑151 (MQ=255)                                       cgcgCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTc                                                                                                          >  2:625466/1‑149 (MQ=255)                                        gcgcCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGc                                                                                                       >  1:697859/1‑151 (MQ=255)                                                        cTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCg                                                                                       >  1:946804/1‑151 (MQ=255)                                                          gggacccGCTCTCCATCTTCTGACAAAGCCTCCCCAGTAG‑CGGTGTTACATAAATGTGA‑TGTTTTTCCGCCAGCGT‑TC‑CCAGA‑TGCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCttt                                                                                         <  1:600260/141‑1 (MQ=255)                                                              ggcGCTCTCCATCATCTAATCAGGCCGGGCCACTAA‑CGGTGCTACAAAAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CAAGA‑TGCAAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATcc                                                                                 <  1:368548/149‑1 (MQ=255)                                                                  ctctCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCg                                                                             >  2:693388/1‑151 (MQ=255)                                                                      ccATCATCTGACCAGGCCGTCCCATTAA‑CGGTGCTACATAAATGTGA‑TGCTTTTTCGCCAGCAG‑TC‑CAAGA‑TGAAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATc                                                                                  <  1:12528/142‑1 (MQ=255)                                                                      ccATCATCTGACCAAGCCGT‑CCACCAAGCGGTGCTACATCAATGTGA‑TGCTTTTTCGCCAGCAG‑TC‑CCAGA‑TGCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGc                                                                              <  1:917499/146‑1 (MQ=255)                                                                        atcatcTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTgg                                                                       >  1:323023/1‑151 (MQ=255)                                                                         tcatcTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGt                                                                      >  1:219420/1‑151 (MQ=255)                                                                             cgtatgaaGCCGTCCCACTAG‑CTGTTCAACATAAATGTGA‑TGCGTTTTCGCCGCGTT‑TT‑CCAGA‑TGCAACCCCCCCACCGCCAGTGGCGTTCGCAGTTTGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAg                                                                   <  2:343451/144‑1 (MQ=255)                                                                              cgATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGc                                                                 >  2:359630/2‑151 (MQ=255)                                                                               gagaaccccGTCCCAATAC‑CGGGGATACATCATTGGGA‑TTCTTTTTCCCCGGCAT‑TC‑CAAGA‑AGCAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGc                                                                 <  1:666377/143‑1 (MQ=255)                                                                                aTCAGGCCGTGCCCTTAG‑CGGGGTTACATCAAGGTGA‑TGCTTTTCCCCCAGCAG‑TC‑CAAGA‑GGCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAgg                                                                  <  2:504808/148‑1 (MQ=255)                                                                                aTCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCg                                                                >  2:136159/1‑150 (MQ=255)                                                                                aTCAAGCCGTGCCACGAA‑GGTTGCTACACGATTGTGT‑TGCTTTTTCGCCGGCAT‑TC‑CAAGA‑GCCAACCGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGc                                                                 <  1:698280/149‑1 (MQ=255)                                                                                aTCAAGCCGGCCCACTAA‑CGGTGCTACATCAATTTGA‑TGCGTTTTCGCCACCAG‑TT‑CCAGG‑TGCAAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCg                                                                <  1:92092/150‑1 (MQ=255)                                                                                   aaGCCGTGCCACTAG‑CGGTGCTACATAAATGTGA‑TGCTTTTTCGCCAGCGG‑TC‑CCAGA‑TGCAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGAc                                                              <  1:723226/149‑1 (MQ=255)                                                                                      ccGTGCCCCAAA‑GGTTGCTACACAAGTGGGA‑TGCTTTTCCGCCAGCGG‑TC‑CAAGA‑GGAAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGa                                                               <  2:827188/145‑1 (MQ=255)                                                                                      ccGTGCAACTAA‑GGGGACAACACAAATGTGA‑TGCGTTTCCGCC‑GCCG‑TTCCCAGA‑TCCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAcg                                                         <  2:47222/151‑2 (MQ=255)                                                                                        gggCCACAAA‑CGGGCCTAAATCAGTGTG‑‑GGGGTTTTCCCCCGTAG‑GT‑CCAGAGTGAAAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAcc                                                         <  2:301674/147‑1 (MQ=255)                                                                                          gCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAcc                                                         >  1:968376/1‑147 (MQ=255)                                                                                           ccACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAc                                                          >  1:838837/1‑145 (MQ=255)                                                                                            cACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAcc                                                         >  2:161971/1‑145 (MQ=255)                                                                                                 aagggggCTACAACAAT‑TGAGTGCGTTTTCGCC‑GTAGTTT‑CCGAA‑GGCAAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGttt                                                <  2:750344/144‑1 (MQ=255)                                                                                                    ggTGCTACATAAATGTGA‑TGCGTTTTCGCCAGCAT‑TT‑CAAGA‑TGAAAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTaa                                              <  1:326327/149‑1 (MQ=255)                                                                                                     gTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGc                                           >  1:503759/1‑151 (MQ=255)                                                                                                       gCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCg                                         >  2:371893/1‑151 (MQ=255)                                                                                                               aaTGTGA‑TGCTTTTTCGCCAGCAT‑TC‑CCAGA‑TGCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAaccacc                                 <  1:167855/151‑1 (MQ=255)                                                                                                               aaTGTGA‑TGCTTTTTCGCCAGCAG‑TC‑CCAGA‑TGAAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAaccacc                                 <  1:285648/151‑1 (MQ=255)                                                                                                                aTGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAaccacc                                 >  1:947628/1‑150 (MQ=255)                                                                                                                 tgtgT‑TGCTTTTCCGCCGGCAG‑TC‑CAAGA‑GGAAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCg                                <  1:513460/150‑1 (MQ=255)                                                                                                                      ttGCTTTTCCCCCAGCAG‑TC‑CAAGA‑TGCAACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCtt                             <  2:305466/148‑1 (MQ=255)                                                                                                                       tGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCg                           >  1:13533/1‑150 (MQ=255)                                                                                                                               cGCCAGCAG‑TT‑CCAGA‑TGCAAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAg                   <  1:61589/150‑1 (MQ=255)                                                                                                                               cGCCAGCAG‑TC‑CCAGA‑TGCAACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAg                   <  1:840243/150‑1 (MQ=255)                                                                                                                                  cggcat‑TT‑CCAGA‑TGAAAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTc                      <  2:139254/142‑1 (MQ=255)                                                                                                                                                  tGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATgg  >  2:718671/1‑151 (MQ=255)                                                                                                                                                           |                                                                                                                                              CATGTTGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAA‑CGGTGCTACATCAATGTGA‑TGCGTTTTCGCCAGCAG‑TT‑CCAGA‑TGCAAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGG  >  NC_000913/4332642‑4332932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑