Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,465,167	0	G	T	43.6%	72.7 / 28.9	55	C29F (TGT→TTT)	gspM	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (6/25);  new base T (24/0);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 2.42e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGCCCA  >  NC_000913/3465021‑3465310                                                                                                                                                   |                                                                                                                                                cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGGTTTTTTTTgg                                                                                                                                             >  2:918023/1‑151 (MQ=255)      gAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCCGCGTTTTTTTTttggttgg                                                                                                                                        >  2:824381/1‑151 (MQ=255)       aaaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTGGCTTggg                                                                                                                                       >  2:725960/1‑151 (MQ=255)       aaaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTggg                                                                                                                                       <  1:457979/151‑1 (MQ=255)       aaaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTggg                                                                                                                                       <  1:994518/151‑1 (MQ=255)        aaaaaCAGAAACAGATCCGGCAAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGTCACTGGCGGATTATTCGTTCCGCGCTTTTTGTTGGCCTgggg                                                                                                                                      >  1:1032070/1‑151 (MQ=255)        aaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTgggg                                                                                                                                      <  1:343247/151‑1 (MQ=255)           aaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCGGCGTTTTTTTTTTGGTTgggggg                                                                                                                                    >  2:31778/1‑148 (MQ=255)               gAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGGTTTTTTTTGGCTTGGGGGGGTaa                                                                                                                                >  2:177906/1‑150 (MQ=255)                aaaaaGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCGGCGGTTTTTTTTTGGGTGGGGGGATaaa                                                                                                                               >  2:325912/1‑150 (MQ=255)                 aaaaGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTGGGTTGGGGGGGTaaaa                                                                                                                              >  2:721027/1‑150 (MQ=255)                   aaGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGGTCTCTCCCCCGGCGGTTTTTTTTTGCTTTGGGGGGTAAAAcc                                                                                                                            >  1:298766/1‑150 (MQ=255)                      aTCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCgata                                                                                                                        <  1:820355/151‑1 (MQ=255)                          ggTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCTCGGCGGTTTTTTTTGGCTTGGGGGGGTAAAACCga                                                                                                                          >  2:652337/1‑145 (MQ=255)                            tCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCCCGGCGTTTTTTTTTGGGTTTGGGGGATAAAAACGACAGATAcc                                                                                                                  >  1:890560/1‑151 (MQ=255)                             cAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATAcc                                                                                                                  <  2:261467/150‑1 (MQ=255)                             cAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCt                                                                                                                 <  1:259701/151‑1 (MQ=255)                                tggtgTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGGTTTTTTTTGGCTTGGGGGGGTAAAACCGATAGATACCTAc                                                                                                               >  2:356087/1‑150 (MQ=255)                                 ggtgTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTGGCTTGGGGGGAAAAAAACgatagataac                                                                                                                  >  2:563587/1‑144 (MQ=255)                                 ggtgTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACa                                                                                                              <  2:999900/150‑1 (MQ=255)                                 ggtgTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCCCGGCGGTTTTTTTTGGCTTGGGGGGATAAAACCGATAGATACCTACa                                                                                                              >  2:283365/1‑150 (MQ=255)                                   tgtATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGGGGTTTTTTTTGGGTTGGGGGGGGAAAACAGATAGATACCTACCtt                                                                                                            >  1:366597/1‑150 (MQ=255)                                      aTGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCag                                                                                                        <  2:432332/151‑1 (MQ=255)                                      aTGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCag                                                                                                        <  1:14035/151‑1 (MQ=255)                                           cAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTTGCTTGGGGGGATAAAAACGATAGATACCTACATTGCAGAGCa                                                                                                    >  2:515613/1‑150 (MQ=255)                                              tAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTTGGTTGGGGGGATAAAAACGATAGATACCTACATTTCaga                                                                                                       >  2:985456/1‑144 (MQ=255)                                                       cAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCCCGCCCGGCGGTTTTTTTTGGCTTGGGGGGGTAAAACCCATAGATACCCACATTGCAGAGCATCAGGccc                                                                                            >  2:713683/1‑146 (MQ=255)                                                           gAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCTCGGCGGTTTTTTTTTGCTTGGGGGGGTAAAAACGATAGATACCCACATTTCAGAGCATCAGGCCCACccgc                                                                                      >  2:293017/1‑148 (MQ=255)                                                            aaaTGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCaaaa                                                                                  <  1:62477/151‑1 (MQ=255)                                                              aTGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGGTTTTTTTTGGCTTGGGGGGGTAAAAACGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCaaaaa                                                                                 >  2:918780/1‑150 (MQ=255)                                                                gATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAAtt                                                                              <  2:694892/151‑1 (MQ=255)                                                                gATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAAt                                                                               <  1:5762/150‑1 (MQ=255)                                                                   tAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTTGCTTTGGGGGGTAAAAACGATAGATACCCACATTTCAGAGCATCAGTCCCCCGCGCCAAAAATTaa                                                                            >  2:486284/1‑150 (MQ=255)                                                                   tAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTaa                                                                            <  1:652706/150‑1 (MQ=255)                                                                    aaaTCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGCTCATTCGCTCGGCGGTTTTTGTTGGGTCTGGGTGTTTAAACCAATAAATACCTACACTGTTAAGCACCAGTTCCACGCGCCAAAAAATaa                                                                            >  1:337568/1‑149 (MQ=255)                                                                                    aaaaaTCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGAt                                                          <  1:343857/151‑1 (MQ=255)                                                                                    aaaaaTCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGAt                                                          <  2:194313/151‑1 (MQ=255)                                                                                    aaaaaTCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCTCCGCGGTTTTTTTTGGCTTTGGGGGATAAAAACCATAGAAACCTACATTGCCGAGCATCAGTCCCCCGCGCAAAAAATTAAGAAAGACATCaaa                                                               >  2:350019/1‑146 (MQ=255)                                                                                        aTCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCACCCGGCGGTTTTTTTTTGGTTGGGGGGATAAAAACGAAAAATACCTACATTGGAGAGCACCAGGCCCCCGCGCAAAAAATTAAGAAGAACAACAAAAGGATGc                                                        >  2:266999/1‑149 (MQ=255)                                                                                          ccACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAgg                                                     <  2:335747/150‑1 (MQ=255)                                                                                           cacaTCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCGGCGGTTTTTTTTTGGTTGGGGGGATAAAAACCATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAAATAAAAAAGACATCAAAAGGATGCAgg                                                     >  2:804758/1‑149 (MQ=255)                                                                                                  gAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGa                                            <  2:588624/151‑1 (MQ=255)                                                                                                   aaaaaCAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCCGCGGTTTTTTTTGGCTTGGGGGGGTAAAAACGATAGATATCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAAATAAGAAGGAAATCAAATGGATGCAGGAGCaa                                                >  2:262997/1‑146 (MQ=255)                                                                                                     aaaCAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCa                                         <  1:95961/151‑1 (MQ=255)                                                                                                           aTCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATg                                   <  2:311808/151‑1 (MQ=255)                                                                                                             cGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGt                                 <  2:672655/151‑1 (MQ=255)                                                                                                              gTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTTTTGGCTTGGGGGGATAAAAACGATAGATACCTACATTGCAGAGCATCAGGCCCCCCCGCCAAAAATTAAGAAAGACATCAAATGGAAGCAGGGTCAAGCGAGCACCCATgg                                  >  2:283275/1‑149 (MQ=255)                                                                                                                    gCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCg                          <  2:765401/151‑1 (MQ=255)                                                                                                                       cTGGCGGTTCTCTCGCTCGGCGGTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCggac                       >  2:540098/1‑149 (MQ=255)                                                                                                                                  ctcgctcgGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTgcgc              <  2:830178/149‑1 (MQ=255)                                                                                                                                  ctcgctcgGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCtt            >  2:633261/1‑151 (MQ=255)                                                                                                                                     gctcgGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACg         <  2:798719/151‑1 (MQ=255)                                                                                                                                        cgGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGc        <  1:292882/149‑1 (MQ=255)                                                                                                                                          gCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGcc    >  1:492803/1‑151 (MQ=255)                                                                                                                                            gTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGCCCa  <  2:183424/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                CGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGCCCA  >  NC_000913/3465021‑3465310

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: ‑