Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,333,757	0	T	G	42.9%	79.5 / 13.2	51	G16G (GGT→GGG)	ispB	octaprenyl diphosphate synthase
Reads supporting (aligned to +/- strand):  ref base T (5/23);  new base G (21/0);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 2.87e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCATTTTTTCAGTACAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGC  >  NC_000913/3333611‑3333905                                                                                                                                                   |                                                                                                                                                      gCCATTTTTTCAGTACAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGgtggt                                                                                                                                                    >  1:88593/1‑148 (MQ=255)      tttttCAGTACAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGc                                                                                                                                               <  1:880610/150‑1 (MQ=255)            aGTACAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATc                                                                                                                                        <  1:635520/151‑1 (MQ=255)               aCAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCtt                                                                                                                                     <  2:715027/151‑1 (MQ=255)               aCAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTAAAGCGGGAAACCtt                                                                                                                                     >  2:813587/1‑151 (MQ=255)                cAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTg                                                                                                                                    <  1:205900/151‑1 (MQ=255)                 aaTCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATAAGGCCATCCtt                                                                                                                                     >  1:77853/1‑149 (MQ=255)                 aaTCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTAATGTgggga                                                                                                                                          >  2:5745/1‑141 (MQ=255)                 aaTCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAATGCGGCAATCCtt                                                                                                                                     >  2:857313/1‑149 (MQ=255)                  aTCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGag                                                                                                                                  <  2:725263/151‑1 (MQ=255)                  aTCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGGGAATATGGCaaagctt                                                                                                                                     >  1:420362/1‑143 (MQ=255)                    cACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGagca                                                                                                                                <  2:216028/151‑1 (MQ=255)                     aCCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTATGAGGCAAACCTTGagc                                                                                                                                 >  1:901938/1‑149 (MQ=255)                     aCCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAAAGCGGCaaacatt                                                                                                                                     >  1:958467/1‑140 (MQ=255)                         tataTTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGCAGGTAATGCAGCAAtgactgcag                                                                                                                                 >  2:856879/1‑137 (MQ=255)                              tCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTc                                                                                                                      <  2:967667/150‑1 (MQ=255)                               ccTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTGATGGGGGAAAACTTGagaaggt                                                                                                                             >  1:623831/1‑141 (MQ=255)                               ccTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTcc                                                                                                                     <  1:944040/150‑1 (MQ=255)                               ccTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCg                                                                                                                    <  1:58292/151‑1 (MQ=255)                                           cccTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGa                                                                                                        <  2:551438/151‑1 (MQ=255)                                                         tGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTAATTTGGGCATCCTTGAGCAGC‑TTTATTTCGGCGGCCCACTGGTTAAACAGTTa                                                                                             >  2:159763/1‑148 (MQ=255)                                                             cacaGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTAtt                                                                                      <  1:1483/151‑1 (MQ=255)                                                             cacaGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTATTGGGGAATCCTTTAGCCGC‑TTTATTTCGACGTCCAACTGATCAATCAGtttaggtatt                                                                                      >  2:207738/1‑143 (MQ=255)                                                                 gTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAAAGGGGGAAAACTTTAGCAGC‑TTAATTTCGACGTCCAACTGATCAAACAGTTAGGGTATTACa                                                                                   >  1:803309/1‑150 (MQ=255)                                                                   aaGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTATTCGGCAAACCTTGAGCAGC‑TTAATTTCGACGTCCCACTGATCAATCAGTTAGGCTAtt                                                                                      >  2:386329/1‑145 (MQ=255)                                                                     ggTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTc                                                                              <  1:992743/151‑1 (MQ=255)                                                                     ggTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTc                                                                              <  1:311794/151‑1 (MQ=255)                                                                     ggTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTATTCGGGAAACCTTTTGCAGG‑CTTATTTCGCCGTCCCACTGATCAAATAATTAGGGTATTTAATCGt                                                                               >  1:534339/1‑150 (MQ=255)                                                                        aaTCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAATGCGGGAAAACTTTAGCAGC‑TTAATTTCCACGCCCCACAGCTCAATCAGTTAGGGTATTACAtact                                                                               >  1:411319/1‑144 (MQ=255)                                                                           aagtgaggaaaGCCCGGCTTTTGCGATGAATTTAGAAAGAATCAAAGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGGCCAACTGATCAAACAGTTAGGCTATTACATCGTCAgcgg                                                                         <  1:589809/142‑1 (MQ=255)                                                                             gggCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTAATGTGGGAAACCTTTAGCAGC‑TTAATTTCGACGTCCAACTGATCAAACAGTTAGGGAATTATATTGTCAgcggcgg                                                                      >  1:771743/1‑151 (MQ=255)                                                                               gCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTATTCGGCAATCCTTTAGCAGC‑TTAATTTCGACGTCCAAATGATCAAACAGTTAGGCGATTACATCCTCAgcggcggcg                                                                    >  2:734569/1‑151 (MQ=255)                                                                               gCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAATGCGGCGAACCTTTAGCCGC‑TTAATTTCGACGTCCAACTGATCAAACAGTTTGGGTATTATATCGTCAgcggggggg                                                                    >  1:494665/1‑149 (MQ=255)                                                                                 gAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTATACGGCAAACCCTTAGCAGC‑TTAAATCCCCCGGCCCACCGATCAATCAGTTAGGCTATTACATCGTCAGcggcggcggg                                                                  >  1:307575/1‑150 (MQ=255)                                                                                    aaGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGAGTTTATATGGGAAACCTTTAGCCGC‑TTAATTTAGACGGTCCACTGATTAATAAGATATGGTTTTACATCTTCCGcggcggggggg                                                                 >  1:188667/1‑147 (MQ=255)                                                                                     aGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAAc                                                              <  2:984739/151‑1 (MQ=255)                                                                                        ccGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTATGCGGGCATCCTTTTGCCGC‑TTAATTTCGACGTCCAACTGATCAAACAATTAGGGTATTACATCTTCAGCGGGGGGGGGaaaa                                                              >  2:872411/1‑147 (MQ=255)                                                                                         cGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAATTCGGGAAACCTTGAGGAGC‑TTAATTTCCACGGCCAACTGATCAATCAGTTAGGGTATTACAACGTCAGcggcgggggggaaagga                                                           >  2:715452/1‑142 (MQ=255)                                                                                           gCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGGTAATAAGGCAAACCTTTAGCAGC‑TTAATTTTGACGGCCCACTGATAAATCAGTTAGGGTATTACATTCTCAGcggcgggggggaaaggatt                                                         >  1:729188/1‑140 (MQ=255)                                                                                               ttGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTATTGGGCAATCCTTTAGCAGC‑TTAATTTCGACGGCCCACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGGAAACGAATTCGttc                                                    >  2:915149/1‑149 (MQ=255)                                                                                                tGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTcc                                                    <  2:623890/150‑1 (MQ=255)                                                                                                tGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTcc                                                    <  2:411557/150‑1 (MQ=255)                                                                                                    aTGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCgatga                                               <  1:671234/151‑1 (MQ=255)                                                                                                       aaTTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTg                                            <  1:425696/151‑1 (MQ=255)                                                                                                          ttAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCt                                          <  2:318438/150‑1 (MQ=255)                                                                                                             gAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTAATCGGCAAACCTTTAGCAGC‑TTAATTTCGACCTCCCACTGATCAAACAGTTTGGCTATTATATCGTCAGCCGCGGCGGGAAAAGGATTTTTCCGGTGAtt                                             >  2:617269/1‑144 (MQ=255)                                                                                                                  aaTCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTATACGGCCAACCCTGAGGAGC‑TTTATTTCCACGCCCCACTGATCAATCAGTTAGGGTATTACATCGTCAGCGGGGGGGGGGAACGTATTTTTCCGCTGGTTGCTGTACTg                                    >  2:605747/1‑148 (MQ=255)                                                                                                                   aTCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTg                                <  2:731157/151‑1 (MQ=255)                                                                                                                    tCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTAATTCGGGAAAACTTTAGCAGCGTTAATTTC‑ACGTCCAACTGATCAATCAGGTAGGGTATTACATCCTCAGCGGCGGGGGGGAAAGGATTTGTCCCGTGAtt                                             >  2:578828/1‑137 (MQ=255)                                                                                                                                    gcAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTAt               <  2:789880/151‑1 (MQ=255)                                                                                                                                         atatGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAggg          <  2:379139/151‑1 (MQ=255)                                                                                                                                               cGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATgc    >  1:24326/1‑151 (MQ=255)                                                                                                                                                  gtgtTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATgcgc  >  2:467307/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                      GCCATTTTTTCAGTACAATCACCCTATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATGCGGCAATCCTTGAGCAGC‑TTAATTCCGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGC  >  NC_000913/3333611‑3333905

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑