Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,177,748	0	C	A	43.4%	59.0 / 31.7	53	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (23/7);  new base A (0/23);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 3.44e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGT  >  NC_000913/3177602‑3177894                                                                                                                                                     |                                                                                                                                                    ttCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGCAGCAA‑GACTGCGGCGTGACCGCGCTCaaa                                                                                                                                                  >  2:358426/1‑150 (MQ=255)     cccTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑ttt                                                                                                                                            >  1:143363/1‑151 (MQ=255)           tCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCccgc                                                                                                                                       <  2:42333/150‑1 (MQ=255)                 atcCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCt                                                                                                                                >  1:64823/1‑151 (MQ=255)                      ggCACCCATCCCCAGTAGCCAGGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGa                                                                                                                           <  2:247431/151‑1 (MQ=255)                      gcaacccacccccAGTAGCCAGGGGTTTGCGGTGGTGTCGTCCGGGGCAACCCGAATCTGCTCAATCAGCACAACTC‑CACCCCGCACTGGGTAAAAGGGTAGCAA‑GCCTGCGGCGTGCCCGCGCTAAAAAA‑TTCCCCGCCGCACCTCATg                                                                                                                            <  1:707287/139‑1 (MQ=255)                         aaCCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTc                                                                                                                        >  2:54439/1‑151 (MQ=255)                                 ccAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGccc                                                                                                                >  1:1077880/1‑151 (MQ=255)                                 ccAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTCCTCAATCAGCACAACTT‑CATCCCGCACTGGGTAAAAGGGTGGCAA‑GCCTGCGGCGTGCCCGCGCTAAAAAT‑TTCCCCGCCGCACCTCATGACTCATTTGc                                                                                                                  <  2:919746/149‑1 (MQ=255)                                    gTAGCCAGGGGGTTTCGCTGGTGTCGTCCGCGGCAACCCGAATCTGCTCAACCACCACAACTT‑CACCCCGCACTGGTTCAAGGGGTAGCAA‑GTCTGCGGCGTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATTACTCATTTGCCCGtt                                                                                                             <  1:495442/151‑1 (MQ=255)                                    gTAGCAAGGGGTTTTCGCTGGTGCCGTACGCGGCAATCCGAATCTGCTCAATCAGCACACCTT‑CACCCCGCACTGGGTCAAAGGGTAGCAA‑GCCGGCGGCGTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGt                                                                                                              <  1:678756/150‑1 (MQ=255)                                        ccAGGGGTTTTCGCTGGTGTCGTCCGGGGCAATCCGAATCTGCTCAATCAGCACACCTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTAAAAAA‑TTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGaa                                                                                                          <  2:2937/150‑1 (MQ=255)                                         cAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAAt                                                                                                         >  1:965093/1‑150 (MQ=255)                                                   cGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGCCCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGAc                                                                                               <  2:505042/150‑1 (MQ=255)                                                    gCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACg                                                                                              >  2:1063255/1‑150 (MQ=255)                                                    gCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACg                                                                                              >  2:191393/1‑150 (MQ=255)                                                      tGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGaa                                                                                            >  1:423836/1‑150 (MQ=255)                                                       ggTGTCGTGCGCGGCAACCCGAATCTGCTAAATCAGCACAACTT‑CATCACGCACGGGGTCAAAGGGTAGCAA‑GCCTGCGGGGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGaa                                                                                            <  2:873871/149‑1 (MQ=255)                                                             gcccgcgGCAATCCGAACCTCCCAAATCAGAACAACTC‑CACCCCGCCCTGGGACAAAGGGTATCAA‑AACGGCGGCGTGCCCGC‑CACAAAAATTTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCtat                                                                                      <  2:830078/146‑1 (MQ=255)                                                             gTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCtat                                                                                      >  1:1119387/1‑149 (MQ=255)                                                               actcgctaacccaaaTCTCCTCAATCAGCA‑AACTTCCACCACGCCCTGGGTC‑AAGGGTTTCAAGGCCGGCGGCGTGACGGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCt                                                                                        <  2:851130/132‑1 (MQ=255)                                                                cgcggaatcccGAATCGGCTCAATCAGCACACCTT‑CACCCCGCACTGGGTAAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATaaa                                                                                   <  2:633010/140‑1 (MQ=255)                                                                 gcgGCAAACCTACTCTGCTAAATAAGCCCACTTT‑CCCCACGCACTGGTTCAAAGGGTAAAAA‑GGCTGGGGCGTACCCGCGCTAAAAAA‑TTCCCCGCCTCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGa                                                                                 <  1:773481/150‑1 (MQ=255)                                                                  cgGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATaa                                                                                    >  2:297541/1‑146 (MQ=255)                                                                    gCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCt                                                                              >  1:819721/1‑150 (MQ=255)                                                                      aaTCCGAATCTGCTCAATCAGCACAACTC‑CATCCCGCACTGGGTAAAGGGGTAGCAA‑GACTGCGGCGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTa                                                                             <  1:1032414/149‑1 (MQ=255)                                                                               cTGATCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaaaaaa                                                                    >  2:537036/1‑149 (MQ=255)                                                                                tGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGc                                                                 >  2:228297/1‑151 (MQ=255)                                                                                     aaTCAGCACAACTT‑CATCACGCATTGGCTAAAAGGGTAGCAA‑GACTGCGGCGTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCcgc                                                              <  2:612752/149‑1 (MQ=255)                                                                                       tCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGAt                                                           <  2:574422/150‑1 (MQ=255)                                                                                         acaacaACTC‑CACCCCGCACTGGGTCAAAGGGTAGCAA‑GCCGGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATa                                                          <  2:954846/146‑1 (MQ=255)                                                                                            acaACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGCTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAgtg                                                     >  2:387921/1‑151 (MQ=255)                                                                                                    catcaCGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCg                                              >  2:8917/1‑151 (MQ=255)                                                                                                     accacgcacgGGGTAAAAGGGTAGAAA‑GACTGCGGCGTGACCGCGCAAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGTCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTtct                                                <  1:189223/146‑1 (MQ=255)                                                                                                       cccGCACTGGGTCAAGGGGTAGCAA‑GCCTGCGGCGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTg                                            <  2:882765/148‑1 (MQ=255)                                                                                                       cacgcacgGGGTAAAAGGGTAGCAA‑GACTGCGGCGTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTg                                            <  2:831484/150‑1 (MQ=255)                                                                                                       caCGCACTGGGTCAAAGGTTAGCAA‑GACTGCGGCGTACCCGCGCACAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCg                                              <  1:285183/148‑1 (MQ=255)                                                                                                            aCTGGGTCAAAGGGTAGCAA‑GACTGGGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCaataa                                      <  2:683064/151‑1 (MQ=255)                                                                                                            aCTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCCAAAA‑TTTACCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTAAAAAGATCTAATGAAAAAAACCCGCGATAAAGTGTTTCTCGTGCaa                                         >  1:109386/1‑148 (MQ=255)                                                                                                               gggTCAAAGGGTAGAAA‑GACTGCGGCGTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCaataat                                     <  2:688952/149‑1 (MQ=255)                                                                                                                gtccAAAGGGTAGAAA‑GACGGCGGCGTGCCCGCGCTAAAAAA‑TTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTc                                  <  1:149819/148‑1 (MQ=255)                                                                                                                    aaaGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTAc                               >  2:781440/1‑150 (MQ=255)                                                                                                                        ggTAGCAA‑GACTGCGGCGTGACCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGt                          <  2:403758/151‑1 (MQ=255)                                                                                                                        ggTAGCAA‑GACGGCGGCGTGCCCGCGCTAAAAAA‑TTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGt                          <  2:486616/151‑1 (MQ=255)                                                                                                                            gCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGttttt                      >  1:104571/1‑151 (MQ=255)                                                                                                                                   cTGCGGCTTGCCCGCGCTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCaa                 <  1:124865/150‑1 (MQ=255)                                                                                                                                       ggcgTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGt             >  1:201884/1‑150 (MQ=255)                                                                                                                                              ccGCGCTAAAAAA‑TTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTaa           <  1:873370/145‑1 (MQ=255)                                                                                                                                                 cgcTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGTCGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGt  >  2:950150/1‑151 (MQ=255)                                                                                                                                                 cgcTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGt  >  1:1039552/1‑151 (MQ=255)                                                                                                                                                 cgcTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGt  >  2:747115/1‑151 (MQ=255)                                                                                                                                                 cgcTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGt  <  1:217632/151‑1 (MQ=255)                                                                                                                                                  gcTAAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGGTAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAgg   <  1:193618/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    TTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTT‑CATCACGCACTGGGTCAAAGGGTAGCAA‑GACTGCGGCGTGACCGCGCTCAAAAA‑TTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGT  >  NC_000913/3177602‑3177894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑