Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,911,754	0	T	G	50.9%	63.6 / 81.0	53	T275P (ACC→CCC)	htpX	putative endopeptidase
Reads supporting (aligned to +/- strand):  ref base T (7/19);  new base G (27/0);  total (34/19)
Fisher's exact test for biased strand distribution p-value = 5.53e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.08e-07

GTGTCAGTGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAGCGCGGCAATCATTTTCTCGCGACCAACCAGTTTTGCCGAACCGGCATCA  >  NC_000913/1911606‑1911902                                                                                                                                                     |                                                                                                                                                       gtgtCAGTGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtgggt                                                                                                                                                        <  2:902988/149‑1 (MQ=255)     cAGTGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGaa                                                                                                                                                  <  1:80083/151‑1 (MQ=255)      aGTGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGaa                                                                                                                                                  >  1:25015/1‑150 (MQ=255)        tGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaaca                                                                                                                                                >  1:747655/1‑150 (MQ=255)          gTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGaacaa                                                                                                                                               >  1:546400/1‑149 (MQ=255)           tttACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATACACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaacaa                                                                                                                                               >  1:737332/1‑148 (MQ=255)              aCGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaacca                                                                                                                                               >  2:44193/1‑143 (MQ=255)                  aTCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGc                                                                                                                                     <  1:777506/151‑1 (MQ=255)                     aCTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGAt                                                                                                                                  <  2:864081/151‑1 (MQ=255)                        cAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGAttt                                                                                                                                <  2:1185192/150‑1 (MQ=255)                            cACGATCCAGGGCATAATAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGCTTTCGAc                                                                                                                            >  2:114374/1‑150 (MQ=255)                                aTCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAAAAACTCACTGAGCGATTTCGACTTAcc                                                                                                                       >  1:1012299/1‑151 (MQ=255)                                aTCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTCGACTTAcc                                                                                                                       >  1:408187/1‑151 (MQ=255)                                      ggCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTaa                                                                                                                 >  1:187205/1‑150 (MQ=255)                                       gCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATg                                                                                                               <  1:538994/151‑1 (MQ=255)                                          tAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAAATCACTGAGCGATTTCGACTTACCG‑TTAAt                                                                                                                >  2:76990/1‑147 (MQ=255)                                          tAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATg                                                                                                               >  1:113919/1‑148 (MQ=255)                                            aaaaaaGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACACACTGAGCGCTTTTGACTTACCG‑TTAATGGag                                                                                                            >  2:711033/1‑149 (MQ=255)                                                aaGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGcc                                                                                                      <  2:605061/151‑1 (MQ=255)                                                 aGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCca                                                                                                     <  1:1173074/151‑1 (MQ=255)                                                   cgcgTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCcatc                                                                                                   <  2:1018703/151‑1 (MQ=255)                                                         gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTTGACTTTCCG‑TTAATGCAGAGAGCCATCATGc                                                                                               >  1:693309/1‑149 (MQ=255)                                                          aTCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCCTGAACAACTCACTGAGCGATTTCGACTTACCG‑GTAATGCAGAGAACCCTCATggcgg                                                                                            >  1:927828/1‑147 (MQ=255)                                                             aGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTTGACTTACCG‑TTAATGGAGAGAGGCATCATTCT‑GGtt                                                                                         >  2:428147/1‑150 (MQ=255)                                                             aGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTg                                                                                        <  1:423349/151‑1 (MQ=255)                                                                  gcgcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACCTACCG‑TTAATGCAGAGAGGCATCATGCT‑GGGTGcttct                                                                                   >  2:1039423/1‑151 (MQ=255)                                                                   cgcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGcttctt                                                                                  <  2:1118275/151‑1 (MQ=255)                                                                    gcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCCTGAACAAACCACTGGGGGGTTTTGCTTTGCCG‑TTAATGCAGAGGGCCATCAAGCC‑GGTTTtttct                                                                                   >  1:1084966/1‑149 (MQ=255)                                                                    gcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCG‑GTAATGCAGAGAGCCATCATGCT‑GGTTGcttctt                                                                                  >  1:1030826/1‑150 (MQ=255)                                                                      tttttAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAAATCACTTAGCGATTTTGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGcttctt                                                                                  >  2:1123141/1‑148 (MQ=255)                                                                      tttttAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAAAAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGGTGcttcttttg                                                                               >  1:283339/1‑148 (MQ=255)                                                                        tttAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCCTGAAAAACTCACTGAGGGATTTCGACTTACCG‑TTAATGAAGAGAGCCAACAACGT‑GGTTGcttcct                                                                                  >  1:707293/1‑144 (MQ=255)                                                                         ttAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATTAAAAACTCCCTTAGCGGTTTTTACTTTCCG‑CTAATTCAGAGAGCCATTAATCT‑GGTTGGTTCTTTCgg                                                                              >  2:511252/1‑149 (MQ=255)                                                                         ttAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGGACAAATTCATGAGCGGTTTCGACCTACCG‑TTAATGCAGAGAGGCATCAAGCT‑GGTTGCTTCTTGCTGtt                                                                            >  2:906928/1‑151 (MQ=255)                                                                           aGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTc                                                                           <  2:393363/150‑1 (MQ=255)                                                                              aTTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAg                                                                       <  1:1212805/151‑1 (MQ=255)                                                                                ttACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCCCTGAGCGATTTCGACTTTCCG‑TTAATGGAGAGAGCCATCATGCT‑GGGTGCTTCTTGCGGTTCATAGCt                                                                     >  1:289576/1‑151 (MQ=255)                                                                                 tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTTCGGTTCATAGCt                                                                     >  1:583342/1‑150 (MQ=255)                                                                                 tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAAAAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTTCTTCTTTCGGGTCATAGCTg                                                                    >  1:285321/1‑151 (MQ=255)                                                                                     tCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGtt                                                                 <  1:400482/150‑1 (MQ=255)                                                                                      cATATTACTTCAGGTATTGACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGtttt                                                               <  2:26633/151‑1 (MQ=255)                                                                                           tACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAgg                                                           <  2:25014/150‑1 (MQ=255)                                                                                                cAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTTCGGGTCATAGCTGGGTTTCAGgcgc                                                        >  1:984569/1‑148 (MQ=255)                                                                                                     aTTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAgcgc                                                <  2:652760/151‑1 (MQ=255)                                                                                                       tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAgcgc                                                <  1:1030489/149‑1 (MQ=255)                                                                                                       tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCG‑GTAATGGAGAGAGGCATCATGCT‑GGGTGCTTTTTTCGGGTCATTGCTGGGTTTTCGGCGCTGCCGCGCgg                                              >  2:279351/1‑151 (MQ=255)                                                                                                        cACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCAAGCAAAACACACATAACGATTTCGACTTACCGTTTAATG‑AGAAAGCCAACCATCT‑GGTTGGTTGTTTAGGTTTATACGTGGTTTTCCAACGCTGCcgcgcg                                               >  2:962804/1‑149 (MQ=255)                                                                                                         aCCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGAGGGTCATGAACAACCCCCTGAGCGGATTCGAATTAACG‑GTTATGGAGAGAGGCATCATGATGGGTTCCTTTTTG‑GGGTCATAGCTGGTTTTCAGGCGCTGCAGCGCgg                                              >  1:177201/1‑149 (MQ=255)                                                                                                            cGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCCTGAACAACCCACTGAGGGATTTCGACTTACCG‑GTAATGCCGAGGGCCAACATCCT‑GGGTGCTTCTTGCGGTTCACAACTGGTTTTCAGGCGCTGCGGCGCGGCAAt                                          >  2:447263/1‑150 (MQ=255)                                                                                                                       cTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTTAGCGATTTTGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGGTGCTTTTTTCGGGTCCTAGCTGGGTTTTAGGCGCTGCAGCGCGGCAATCATTTTTTcccg                              >  2:475107/1‑151 (MQ=255)                                                                                                                          cAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCCCCGAGCGATTTTCACCTACCG‑GTAATGCAGAGAGCCATCATTCT‑GGGTGCTTCTTTCGGGTCATAGCTGGGTTTCAAGCGCCGCAGCGCGGCAATCATTTTCTCGCGacc                           >  2:571080/1‑151 (MQ=255)                                                                                                                                      ccAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAGCGCGGCAATCATTTTCTCGCGACCAACCAGTTTTg                <  1:654442/150‑1 (MQ=255)                                                                                                                                      ccAGCGGCGGGCGGGGGATGAACAAATAACCGAGCGATTTCGAACTTCCG‑TTAATGGAGAGAGCCATCATGCT‑GGGTGCTTCTTGCGGTTCATAACTGGGTTTCATGCGCCTCAGCGCGGCAATCATTTTCTCCCGGCCAACCAGtttt                 >  2:140334/1‑149 (MQ=255)                                                                                                                                             cggGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAGCGCGGCAATCATTTTCTCGCGACCAACCAGTTTTGCCGAACCg        <  1:914872/151‑1 (MQ=255)                                                                                                                                                   ggtCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAGCGCGGCAATCATTTTCTCGCGACCAACCAGTTTTGCCGAACCGGCATCa  <  1:987033/151‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                       GTGTCAGTGGTTTACGTATCACTCAGCCACGATCCAGGGCATAAAAAAAGCGCGTCGATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCG‑TTAATGCAGAGAGCCATCATGCT‑GGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCAGCGCGGCAATCATTTTCTCGCGACCAACCAGTTTTGCCGAACCGGCATCA  >  NC_000913/1911606‑1911902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑