Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,079,468	0	A	G	40.4%	76.5 / 15.2	52	D55G (GAT→GGT)	putP	proline:sodium symporter
Reads supporting (aligned to +/- strand):  ref base A (5/26);  new base G (21/0);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 6.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATACAACA  >  NC_000913/1079327‑1079617                                                                                                                                               |                                                                                                                                                           tGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGGATGAgggg                                                                                                                                                   >  1:561944/1‑151 (MQ=255)  ggTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGTATGAgggg                                                                                                                                                   >  1:6645/1‑150 (MQ=255)    tGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGTATgggggg                                                                                                                                                   >  1:91750/1‑143 (MQ=255)        aTTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGgctggct‑g                                                                                                                                           <  1:311745/151‑1 (MQ=255)          tttGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑TCGGGTATGTGCGgcggggt‑ggt                                                                                                                                         >  2:185663/1‑149 (MQ=255)             gtgtCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGG‑TCGGGGATGAGGggctgggggtt                                                                                                                                          >  1:644132/1‑143 (MQ=255)             gtgtCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AAt                                                                                                                                    <  1:929699/151‑1 (MQ=255)               gtCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATg                                                                                                                                   <  1:428662/150‑1 (MQ=255)                tCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGGATGGGCGGGTGGGT‑G‑GT‑TATggg                                                                                                                                 >  1:762070/1‑151 (MQ=255)                 cTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGG‑TCGGGTATGAGCGGCGGGCT‑G‑GT‑TATgggg                                                                                                                                >  1:976457/1‑151 (MQ=255)                   atatCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGTG‑TCGGGTGTGAGCGGGTGGGT‑G‑GT‑GATtggg                                                                                                                                >  2:461783/1‑149 (MQ=255)                       cTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGTCG‑TCGGGGATGAGCGGGTGGGG‑G‑GT‑TATGGGGt                                                                                                                               >  2:633095/1‑146 (MQ=255)                         ttGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGc                                                                                                                            <  2:416995/147‑1 (MQ=255)                         ttGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCgg                                                                                                                         <  2:390911/150‑1 (MQ=255)                         ttGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCgg                                                                                                                         <  1:7332/150‑1 (MQ=255)                          tGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGGATGAGCGGGGGGGC‑G‑TT‑TATggg                                                                                                                                 >  2:251575/1‑141 (MQ=255)                               tGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GTGGGGATGAGGGGGGGGGTGG‑TT‑AATGGGGTGGCggggg                                                                                                                       >  1:119519/1‑146 (MQ=255)                                 atatTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑Gttt                                                                                                               <  1:878157/151‑1 (MQ=255)                                 atatTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGTATGAGGGGGCGGCT‑G‑TT‑TATTTGGGTGCCCGgggccggtt                                                                                                                >  2:1046924/1‑146 (MQ=255)                                  tatTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCG‑GCGGGTATTAGAGGCCGGGT‑G‑TT‑TATGGGGGTGGCGGGCGCT‑Ggttt                                                                                                              >  2:1104040/1‑151 (MQ=255)                                   attgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑Gttttt                                                                                                             <  1:172643/151‑1 (MQ=255)                                    ttgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑Gttttt                                                                                                             <  1:90971/150‑1 (MQ=255)                                           ggTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCgg                                                                                                     <  2:6884/151‑1 (MQ=255)                                             tttATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCG‑TCGGGTATGAGCGGGCGGCT‑G‑TT‑TATGGGGGTGCCGGGGGCT‑GGTTTTTTTTTCgggg                                                                                                   >  1:1085601/1‑150 (MQ=255)                                                  cGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTcc                                                                                              <  1:1471/151‑1 (MQ=255)                                                   gCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCg                                                                                             <  1:857235/151‑1 (MQ=255)                                                   gCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCg                                                                                             <  2:565106/151‑1 (MQ=255)                                                      tGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCG‑GCGGGGATTTGGGGGCGGGT‑GTTT‑ATTGGGGTGGCGGGGGGCG‑TTTTTTTTTTCCGGGGtt                                                                                                 >  2:947959/1‑145 (MQ=255)                                                      tGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCG‑GCGGGGATGAGCGGCTGGGG‑G‑TT‑TATTGGGGTGGCGGGCGCT‑GGttttttttttgggggtt                                                                                                >  2:448376/1‑136 (MQ=255)                                                         cGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCt                                                                                       <  1:142440/151‑1 (MQ=255)                                                         cGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GCGGGTATGAGGGGGTGGGT‑G‑GT‑TATGGGGGTGGCGGGGGCC‑GGTTTTTTTTTCGGGGTTTTCGaaa                                                                                          >  1:1057918/1‑148 (MQ=255)                                                            tCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGCGCGGAGATGGGGGGC‑GGCT‑G‑GT‑TATGGGGGGGGCGGGGGCTCGTTTTTTTTCCCGGGtttt                                                                                                >  1:208937/1‑140 (MQ=255)                                                                    aaaCTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCAtt                                                                            <  1:237098/151‑1 (MQ=255)                                                                        tttGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGG‑GGGGGTATGGGGGGCTGGGT‑G‑CT‑CATTGGGGGGTCGGGGGGT‑GGTTTTTTTTTCTGGGTTTCTGAAAGCTGGGTCg                                                                                 >  2:560446/1‑142 (MQ=255)                                                                            acgacTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCG‑TCGGGTATGAGCGGGGGGCT‑G‑TT‑TATGGGGGTGGCGGGGGGT‑GTTTTTTTTTTCGGGGGTTTCGAAAGCTGGGGCGCCCTTGGCCTGAc                                                                    >  1:50674/1‑151 (MQ=255)                                                                                      tCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGgcgc                                                          <  1:315474/150‑1 (MQ=255)                                                                                         gggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGcgcg                                                         <  1:104773/148‑1 (MQ=255)                                                                                         gggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGt                                                        <  1:82822/149‑1 (MQ=255)                                                                                             ggTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTa                                                  <  1:554323/151‑1 (MQ=255)                                                                                                   aGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTgg                                             <  2:408312/150‑1 (MQ=255)                                                                                                     tCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGG‑TCGGGTTTGGGCGGGCGGCT‑G‑GT‑TATGGGGGTGCCGGGGGGG‑GGTTTTTTTTTTGGGGTTTTCGGAAACTGGGTCGCCCCTTGCCTGACA‑TTAGGGGCGGGGGTTTACTgg                                             >  2:163611/1‑148 (MQ=255)                                                                                                           gCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCtggtg                                    <  1:1125472/151‑1 (MQ=255)                                                                                                             cATTCGTGACGGCATTATCGGCGGGTGGG‑GCGGGGATTAGGGGCGGGCT‑G‑TTGATTGGGGTGGCGGGGGGCG‑GTTTTT‑TTTTTGGGGTTTTCGGAAGCTGGGACGCCCTTTGGCTGGCATTTAGGGGGGGGGTTTAACTgatggggggg                                     >  2:889841/1‑140 (MQ=255)                                                                                                                     aCGGCATTATCGGCGGGTGCG‑TCGGAGATGAGGGGCCGGCT‑G‑TT‑AATTGGGGTGCCGGGCGGG‑GTTTTTTTTTTCGGGGTTTTCCGAAGCTGGGGCGCCCCTGGCCCGTCA‑TTAAGCGCGGGGGTTAAATTGGAACTGGGGGCCGGGCgg                           >  1:801104/1‑150 (MQ=255)                                                                                                                      cGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGtt                         <  1:701444/151‑1 (MQ=255)                                                                                                                      cGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGtt                         <  1:203374/151‑1 (MQ=255)                                                                                                                          aTTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCgt                     <  1:536056/151‑1 (MQ=255)                                                                                                                              tCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGGTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGGTGCGtgtg                  >  2:198989/1‑150 (MQ=255)                                                                                                                                ggcggGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGTTTTCCGAAAGCTGGATCGCCATTGGCCTGTCT‑TTAGGCGCGTGGATTAAATGGAAGCTGGTGGCCGGGCGGTTGCgtggg                  >  2:438346/1‑146 (MQ=255)                                                                                                                                 gcggGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATa              <  2:295343/151‑1 (MQ=255)                                                                                                                                             ggATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATacaac   >  1:148796/1‑151 (MQ=255)                                                                                                                                              gATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATacaaca  <  1:290370/151‑1 (MQ=255)                                                                                                                                               atatGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATacaaca  >  2:958472/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                           TGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCG‑TCGGATATGAGCGGCTGGCT‑G‑TT‑AATGGGGTTGCCGGGCGCT‑GTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACA‑TTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATACAACA  >  NC_000913/1079327‑1079617

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑