Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,133,302	0	T	G	42.9%	87.9 / 10.1	56	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (8/24);  new base G (24/0);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 4.75e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACGG  >  NC_000913/3133156‑3133449                                                                                                                                                   |                                                                                                                                                    gTAGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTc                                                                                                                                                  <  2:166103/150‑1 (MQ=255)      tGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCa                                                                                                                                             <  2:950912/150‑1 (MQ=255)       gggCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATc                                                                                                                                           <  1:632702/151‑1 (MQ=255)           tGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTAACCCaatc                                                                                                                                          >  1:704918/1‑145 (MQ=255)           tGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCATc                                                                                                                                           >  2:601513/1‑147 (MQ=255)             cggcgCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCCTCCAggt                                                                                                                                      >  2:550020/1‑148 (MQ=255)              ggcgCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCa                                                                                                                                    <  2:973461/151‑1 (MQ=255)                 gcgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCATCCAGTTTaa                                                                                                                                   >  1:40424/1‑149 (MQ=255)                  cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTGGCCCCTcccctt                                                                                                                                      >  2:628288/1‑141 (MQ=255)                   ggTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGAt                                                                                                                               <  2:940534/151‑1 (MQ=255)                    gTTGAACTATTAGCAGTTTGAGTTTGTAGCGCAGCCATTCGTTAAATCATCCACTACCCTTTTTTGTGGTCAGCAAAGCGCGGCGTGAATTGGCCGTAGTCACGCTTGGAGAATTTCATCGGCGGGGTGTCGGACATTTAGTTCAAg                                                                                                                                  <  2:506030/147‑1 (MQ=255)                         aCTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTGGCCCCTCCAGTTTACGGGTCTTTgt                                                                                                                         >  2:382813/1‑150 (MQ=255)                              tAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCAGTTCAAAGATCTTTTCGcc                                                                                                                      >  1:852779/1‑149 (MQ=255)                               aaCAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCAtt                                                                                                                   <  1:995861/151‑1 (MQ=255)                                  agtttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCAGTTCAAGGATCTTTGCGCCAtt                                                                                                                   >  1:752657/1‑148 (MQ=255)                                      tgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGt                                                                                                             <  1:111292/150‑1 (MQ=255)                                         gtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCCTTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGCAGCGACGCTTGCAGAATTTTATCGGCGGGGGGGCGTTCTTTGCGTTCTAAGATCTTTGCGCCGTTggaagt                                                                                                             >  2:277971/1‑142 (MQ=255)                                                gTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCAGTTTAAGGATCTTTGCGCCATTTAATGTCAGTTgcggcg                                                                                                  >  2:441977/1‑151 (MQ=255)                                                    aTCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCCGTTCAAAGATCTTTGCGCCATTGTATGTCAGTTgcgggggga                                                                                               >  2:338944/1‑145 (MQ=255)                                                       cATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCCGTTCAAGGATATTTTCGCCATTTAATGTCAGGTGCGGCGGAACgg                                                                                            >  1:318229/1‑150 (MQ=255)                                                        aTTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCg                                                                                          <  2:312850/151‑1 (MQ=255)                                                        aTTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCg                                                                                          <  1:82846/151‑1 (MQ=255)                                                            gTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGGGCCCCTCCCGTTTCAGGATCTTTTTGCCCTTTAATGTTAGTTGCGGGGTAACGGCGGttt                                                                                      >  2:50485/1‑151 (MQ=255)                                                              tAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCAGTTCTAGGGTCTTTTCGCCATTGAATGTCAGTTTCGGCGTAAAGGGGGttttt                                                                                    >  1:237072/1‑151 (MQ=255)                                                               aaaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGAtttttt                                                                                   <  1:807681/151‑1 (MQ=255)                                                               aaaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGAttttt                                                                                    <  1:338002/150‑1 (MQ=255)                                                               aaaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCAGTTCAAGGGTCTTTTCGCCCTTGAATGTCAGTTGCGGCGGAAAGGCGAtttttt                                                                                   >  1:252770/1‑151 (MQ=255)                                                               aaaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCCGGTCAAAGGTCTTTTCGCCATTGAATGTCAGTTGCGGCGGAAAGGCGGtttttt                                                                                   >  1:863782/1‑151 (MQ=255)                                                                aaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCCTCCCGTTTCAGGAGCCTTTCGCCATTGGATGTCAGTTGTGGCGTAAAGGGGGtttttt                                                                                   >  1:616909/1‑150 (MQ=255)                                                                          tATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCCCCCCGGTTAAGGAGATTTGTGCCCTTTGATGTTAGTTGGGGGGGAACGGGGGgtttttt                                                                                  >  2:748226/1‑140 (MQ=255)                                                                               aTTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGTGCCCCCCCCGGTCAAAGGTCTTTTCGCCCTTTAATGTCAGTTTTGGCGTGAAGGCGATTTTTTTCTGTAACGCTGCCa                                                                    >  1:467536/1‑150 (MQ=255)                                                                                 tttGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGt                                                                  <  1:50528/150‑1 (MQ=255)                                                                                     gTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTtggtg                                                             <  1:858059/151‑1 (MQ=255)                                                                                     gTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTtggtg                                                             <  2:12344/151‑1 (MQ=255)                                                                                     gTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCCGGTCCAGGATCTTTTCGCCATTGGAAGTCAGTTGCGGCGTAACGGCGGTTTTTTTCTGTAACGCTGCCCGTtgg                                                               >  2:857960/1‑149 (MQ=255)                                                                                       gATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTTGCCCCTCCAGTTCAAAGATCTTTGCGCCATTTAATGTCAGTTTCGGCGGAACGGCGATTTTTTTCTTTAAAGCTGCCAGGtggggg                                                            >  1:653/1‑150 (MQ=255)                                                                                              aaaGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTGGCCCATCCCGCTGAAGGGTATTTTCGACATTGAAGGGCAGGTGCGGGGTAATAGCGCTTTTTTCCTTTTACGCTGGCCGGtggtggggcaggtt                                                    >  2:148804/1‑143 (MQ=255)                                                                                                  cgcgGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTTCCGATCAAGGATGTTTTAGCCCTTGGATTGCCGATGCGGCGTACAGGCGGATTTTTCCTGTAAACCCGGCAGATGGTGGTGAgggt                                                     >  1:29259/1‑144 (MQ=255)                                                                                                     ggcgTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCa                                             <  2:262548/151‑1 (MQ=255)                                                                                                              tGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAAGATCTTTTCGCCATTGAATGTCAGTTGCGGCGTAACGGCGGTTTTTTCCTGTAACGCTGCCCGTTGGTGGGCCGGGTTACGCGCAAAAGCggg                                     >  1:182671/1‑149 (MQ=255)                                                                                                                     aGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTtca                              <  1:574218/150‑1 (MQ=255)                                                                                                                      gTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTtcatc                            <  1:64655/151‑1 (MQ=255)                                                                                                                         aCGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCAGTTTAAGGATCTTTGGGCCATTGAATGTCAGTTGCGGCGTAAAGGCGGTTTTTTTCTGTAAAGCTGCCAGGTGGTGGGCAGGGTTACGCGCAAACGCGGGTTGTTCATCaa                          >  1:133561/1‑150 (MQ=255)                                                                                                                             ttGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCCGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGGAACGGCGATTTTTTCCTGTAAAGCTGCCAGTTGGTGGGCAGGGTTTCGCGCAAACGCGGGTTGTTCATCAATGcc                      >  1:140504/1‑150 (MQ=255)                                                                                                                               gCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCaa                    <  1:49767/150‑1 (MQ=255)                                                                                                                                 aGAATTTCATCGGCGGGGTGTCGCCCCTCCCGTTCAAGGATCTTTGCGCCATTGTATGTCAGTTGCGGGGGAACGGCGGTTTTTTTCTGTAACGCTGCCAGTTGGGGGGCAGGTTTATGCGCAAAAGCGGGTTGTTTATCAATGCCCAGa                  >  2:324235/1‑150 (MQ=255)                                                                                                                                  gAATTTCATCGGCGGGGTGTGCCCCCGCCCGTTCAAGTGTATTTGTGCAATTGATAGGACGGAGCGGCGGAACGGCGATTTTTTCTAGCAACGCTGCCCGTTGGTGGTATGGTTTAATCGCAAACTCGGGTCGGTCTTTAAAGCCaa                    >  2:571937/1‑147 (MQ=255)                                                                                                                                  gAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACg                <  1:351087/151‑1 (MQ=255)                                                                                                                                   aaTTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACg                <  2:118543/150‑1 (MQ=255)                                                                                                                                           cggcggGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATcaacaa       <  2:603245/151‑1 (MQ=255)                                                                                                                                           cggcggGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATcaaca        >  1:24288/1‑150 (MQ=255)                                                                                                                                            ggcggGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAAt      >  1:161485/1‑151 (MQ=255)                                                                                                                                               ggggTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATAc    <  2:342486/150‑1 (MQ=255)                                                                                                                                               ggggTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACg   >  1:531928/1‑151 (MQ=255)                                                                                                                                                gggTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACgg  <  1:61340/151‑1 (MQ=255)                                                                                                                                                gggTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACgg  >  2:15553/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GTAGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCAGTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACGG  >  NC_000913/3133156‑3133449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑