Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,850,007	0	G	A	45.1%	39.6 / 31.5	51	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base G (20/8);  new base A (0/23);  total (20/31)
Fisher's exact test for biased strand distribution p-value = 4.33e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAACATGC  >  NC_000913/3849857‑3850155                                                                                                                                                        |                                                                                                                                                       aCGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACgg                                                                                                                                                        >  2:534823/1‑151 (MQ=255)  cGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACgg                                                                                                                                                        >  1:57821/1‑150 (MQ=255)      aGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATa                                                                                                                                                  <  1:809626/151‑1 (MQ=255)       gTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATa                                                                                                                                                  >  2:953159/1‑150 (MQ=255)                 gATCACCAAGAACGGAAAATGGTTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGc                                                                                                                                       <  2:170881/150‑1 (MQ=255)                        aaTAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATc                                                                                                                                 >  1:520612/1‑149 (MQ=255)                            aCGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGgcg                                                                                                                           >  2:291544/1‑151 (MQ=255)                               gAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTc                                                                                                                        >  1:998627/1‑151 (MQ=255)                                   aTGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAAcc                                                                                                                    >  1:604260/1‑151 (MQ=255)                                      ggTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAAcc                                                                                                                    >  2:670652/1‑148 (MQ=255)                                        ttAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATg                                                                                                               >  1:707410/1‑151 (MQ=255)                                          aacccgcccgcCTGCGTTAGCCAGAAAACCAGCACCCCCCCCGCCCCCAGAAATCGGGGCCAGTACCCGCGCGGGCATTG‑CAGCATTACCCCCAGACGCAGCCCAAACGA‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCa                                                                                                             <  1:191394/148‑1 (MQ=255)                                             ccgcccgcCGGCGTAAGCAAGAAAACCAGCCCCCCCCCCGCGCCCAGAATTCGGGGCCATTCCCCGCGGGGGAATTG‑CAGCATTACCCCCAGACACAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCa                                                                                                             <  2:402168/148‑1 (MQ=255)                                                ccccccTGCGTTGCCAAGAAAACCAGCACCCCCCCCGCCCCCAGAAATCGGGGCCAGTACCCGCGGGGGCATTG‑CAGCATTACCCCCAGCCGCAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGc                                                                                                          <  1:962211/144‑1 (MQ=255)                                                    ccggCGTTACCCATTAAACCAGCCGCCCCCCCCCCCCCAGCAATCCGGCCCAGTACCCGCGCGGGCATTG‑CACCATTACCCCAGGCCGCAGACAAAACGA‑AAATAC‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATa                                                                                                     <  1:861371/146‑1 (MQ=255)                                                         gTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                               >  1:109005/1‑150 (MQ=255)                                                              caaGTAAACCAGCAGCCCCCCCGCGCCCAACAATGCGGGCCAGTACCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACAAAACGA‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGc                                                                                           <  1:170986/147‑1 (MQ=255)                                                                agaaaaCCAGCCCCCACCCCCCCCCCAGCAATACGGGCCATTACCCGCGCGGGCATTG‑CAGAATTAGCCCCGGGACCAGACCAAACGG‑AAATAC‑CGGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCaaa                                                                                        <  1:820607/147‑1 (MQ=255)                                                                    aaccagcacCCCCCCCGCCCCAAGAAATGGGGGCCAGTCCCCGCGCGGGCTTGG‑CAGCATAACCCCCAGACGCAAACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCAt                                                                                   <  1:947111/148‑1 (MQ=255)                                                                       cagcagCCCCCCCGCCCCCAGCAATCCGGGCAAGTACCCGCGGGGGCATTG‑CAGCATTACCCCCAGCCGCACACAAAGCGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGc                                                                                 <  1:157702/150‑1 (MQ=255)                                                                        agcagcCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCgg                                                                               >  2:209793/1‑151 (MQ=255)                                                                             cccccccccccccAGAAATGCGGCCAAGTACCGGCGCGGGAATGG‑CAGCATGCCCCCCGGCCGCA‑ACCAAACCG‑AAAAAACCACCGCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCagag                                                                          <  2:157185/141‑1 (MQ=255)                                                                              ccccccGCCCCCAGCAAACGGGGCAAGTACCCGCGGGGACATGG‑CAGCATACGCCCCAGCCGCAGACAAAAGGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                                         <  1:427594/147‑1 (MQ=255)                                                                                       cccgaaaatcgggcccAGTACCCGGGGGGGTATTG‑CAGAATAGCCCCCAGACGCAACCAAAAAGA‑AAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                                <  2:698151/137‑1 (MQ=255)                                                                                        ccAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                                >  2:283365/1‑150 (MQ=255)                                                                                            cAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                             >  2:671420/1‑149 (MQ=255)                                                                                             aaTACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAgg                                                          >  1:995561/1‑151 (MQ=255)                                                                                                  gggCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAAt                                                      >  1:394905/1‑150 (MQ=255)                                                                                                  gggCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAAt                                                      >  2:263507/1‑150 (MQ=255)                                                                                                     ccAGTACCCGCGGGGGCATGG‑CAGCATAAGCCCCAGACGCAAACAAAAGGA‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAAc                                                   <  1:377486/150‑1 (MQ=255)                                                                                                        gtctCCGCGCGGGCTTAG‑CAACATACCCCCCAGCCGCAACCCAAAGGG‑AAACAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAAc                                                   <  1:956507/144‑1 (MQ=255)                                                                                                         tacccGCGCGGGCATTG‑CAGCATTACCCCCAGACGCAGACCAAACGA‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAAc                                                   <  1:275469/143‑1 (MQ=255)                                                                                                           ccggcgcgGGCATGG‑CACCATACCCCCCAGCCCAACAAAAAACGA‑AAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAtt                                            <  2:132179/148‑1 (MQ=255)                                                                                                            cggggcgGACATTG‑CAGCCTTCGCCCCA‑AGCAACCCCAAACGGAAAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTa                                           <  1:49845/147‑1 (MQ=255)                                                                                                            ccgggggggCATTG‑CAGCATTACCCCCAGACGCAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTa                                           <  1:501841/145‑1 (MQ=255)                                                                                                            ccGCGGGGGCATTG‑CACCATTACCCCCAGCCGAAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAt                                             <  1:22043/149‑1 (MQ=255)                                                                                                                gggggCATTG‑AAGCATTAGCCCCGGGCGCAGACAAAACGA‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAtt                                            <  1:627814/144‑1 (MQ=255)                                                                                                                gcgGTCATGG‑CAGCATTAGCCCCAGACGCAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTaa                                          <  1:775398/148‑1 (MQ=255)                                                                                                                  gggCTTGG‑CAGCATTCCCCCCAGACGCAAACAAAACGA‑AAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAg                                         <  1:945787/147‑1 (MQ=255)                                                                                                                  gggCATTG‑CATCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCggg                                     >  2:124851/1‑151 (MQ=255)                                                                                                                   ggCATTGCCAGCATCCCCCCCAGACGAACCCAAAACAG‑AAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTaa                                          <  2:188791/146‑1 (MQ=255)                                                                                                                   ggCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCggg                                     >  2:773183/1‑150 (MQ=255)                                                                                                                            agcaTTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACg                            >  1:638910/1‑151 (MQ=255)                                                                                                                              cattgcccccAGCCGAAAACAAAAAAG‑AAAAAA‑CAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTc                          <  2:445096/145‑1 (MQ=255)                                                                                                                               aTTACCCCCAGACGAAAACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaacaa                              <  1:264346/146‑1 (MQ=255)                                                                                                                                ttAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt                        >  2:587470/1‑151 (MQ=255)                                                                                                                                 tacccccAGACCAAGACAAAACGA‑AAAAAA‑CGCCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt                        <  1:670441/147‑1 (MQ=255)                                                                                                                                   cccccAGCCGCAGACAAAACGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt                        <  1:666573/147‑1 (MQ=255)                                                                                                                                     cccAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt                        >  2:666556/1‑146 (MQ=255)                                                                                                                                              aGACAAAACGA‑AAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAg               <  2:213037/146‑1 (MQ=255)                                                                                                                                                   aaaCGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCa                <  1:965858/140‑1 (MQ=255)                                                                                                                                                    aaCGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAACAt    >  2:411965/1‑151 (MQ=255)                                                                                                                                                    aaCGA‑AAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACCCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAACAt    <  1:430668/151‑1 (MQ=255)                                                                                                                                                       gg‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAACATgc  >  2:437803/1‑150 (MQ=255)                                                                                                                                                        |                                                                                                                                                       ACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTG‑CAGCATTAGCCCCAGACGCAGACCAAACGG‑AAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAACATGC  >  NC_000913/3849857‑3850155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑