Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,079,468	0	A	G	46.8%	61.6 / 11.0	47	D55G (GAT→GGT)	putP	proline:sodium symporter
Reads supporting (aligned to +/- strand):  ref base A (2/23);  new base G (22/0);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 2.02e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATA  >  NC_000913/1079321‑1079612                                                                                                                                                    |                                                                                                                                                        cGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGatat                                                                                                                                                      <  2:345211/151‑1 (MQ=255) cGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGatat                                                                                                                                                      <  2:375136/151‑1 (MQ=255)      ttGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGc                                                                                                                                                  <  1:740954/150‑1 (MQ=255)       tGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAgggg                                                                                                                                                >  1:898621/1‑151 (MQ=255)          tGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGATGAgggg                                                                                                                                                >  1:842286/1‑148 (MQ=255)             cATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCggctggct                                                                                                                                          <  2:537805/151‑1 (MQ=255)                tttGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑t                                                                                                                                      <  1:204540/150‑1 (MQ=255)                         atatCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑gggg                                                                                                                             <  1:848554/149‑1 (MQ=255)                          tatCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGtt                                                                                                                           <  1:744871/150‑1 (MQ=255)                                  gCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGGTATGAGAGGCCGGCT‑G‑TTTAT‑GGGGGTGGCggggg                                                                                                                   >  2:651907/1‑148 (MQ=255)                                   cATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGGGGGGGGGG‑G‑TTTAT‑GGGGGTGGCggggg                                                                                                                   >  2:671012/1‑147 (MQ=255)                                    aTGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGCTGGTGGTC‑G‑TTAAT‑GTGGGTGTCgcgtgc                                                                                                                  >  1:234173/1‑144 (MQ=255)                                     tGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGGGGGGGATGAGGGGGGGGGT‑G‑TTGAT‑GGGGGTGTGGGgc‑g                                                                                                                  >  2:779590/1‑147 (MQ=255)                                         attgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTCGGGGATGAGGGGGCGGCG‑G‑GTTAT‑GGGGGTGGCGGGG‑G‑C‑CG‑gtttt                                                                                                       >  1:798833/1‑151 (MQ=255)                                           tgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGAGTGCGGTGTGGGGGGCGTGCC‑G‑GTCAT‑GGGGTTGCCGGGCGG‑C‑GG‑tttttt                                                                                                      >  1:914400/1‑150 (MQ=255)                                               tgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTtttctttc                                                                                                  <  1:579122/150‑1 (MQ=255)                                                  gTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCggg                                                                                              <  2:197957/151‑1 (MQ=255)                                                  gTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTCGGGGATGAGGGGGGGGCT‑G‑TTTTT‑TGGGGTGTCGGGG‑G‑C‑GG‑Gttttttttttggg                                                                                              >  1:39434/1‑146 (MQ=255)                                                   tttATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGGGGGGGTGGGT‑G‑TTTAT‑GGGGGTGGCCGGG‑G‑C‑TG‑Ttttttttt                                                                                                   >  1:7354/1‑145 (MQ=255)                                                        cGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTc                                                                                         <  2:408125/150‑1 (MQ=255)                                                           cTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGGGCGGGTATGAGCGGCGGGCT‑G‑TTTAT‑GGGGGTGGCCGGC‑G‑C‑CG‑TTTTTTTTTTCgggggtttc                                                                                        >  2:392554/1‑142 (MQ=255)                                                                gATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTg                                                                                <  2:307911/151‑1 (MQ=255)                                                                gATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGTTGAGGGGCTGGGT‑G‑TTTAT‑GGGGGTGTCGGGG‑G‑C‑GGTTTTTTTTTTCTGGGTTTTCCTaaaac                                                                                  >  2:1000201/1‑148 (MQ=255)                                                                   cAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGGGGGGGTGGCT‑G‑GTTAT‑GGGGGGGTCGGGG‑G‑G‑GG‑GTTTTTTTTTCGGGGTTTc                                                                                         >  1:548090/1‑139 (MQ=255)                                                                    aaCGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATTAGGGGGTGGGT‑G‑TTTAT‑GGGGGTGGCGGGG‑GCC‑GG‑TTTTTTTTTCGGGGGTTTCCGaa                                                                                     >  2:745260/1‑143 (MQ=255)                                                                    aaCGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGTGGGGTATTAGCGGGGGGCG‑G‑TTTAT‑GGGGGTGGCGGGG‑G‑C‑GGTTTTTTTTTTCCGGGTTTTcgtaa                                                                                     >  1:170549/1‑139 (MQ=255)                                                                       gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAGGGGGCGGCG‑GTTTATT‑GGGGTGGCGGGGG‑G‑T‑GG‑TTTTTTTTTCCGGGTTTTCGGaaaccgggtcgcc                                                                          >  2:634169/1‑141 (MQ=255)                                                                       gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTTTGGGGGGGTGGGT‑G‑TTTAT‑GTGGGTGGCGGGC‑G‑CGGG‑TTTTTTTTTCGGGGTTTTCCGAAAGCGGGAtgcc                                                                          >  1:54555/1‑148 (MQ=255)                                                                            aCTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTCGGGTATGAGCGGGGGGGTGG‑TTATT‑GGGGTGGCGGGGG‑C‑C‑GG‑TTTTTTTTTCGGGGGTTTCCCaaaatgggtcgcc                                                                          >  1:1047549/1‑136 (MQ=255)                                                                               ttGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGAGCGGGGGGCT‑G‑TTAAT‑GGGGGTGCAGGGG‑G‑C‑GG‑TTTTTTTTTTCGGGATTTTCGGAAGCTGGAACGcccatgggc                                                                  >  2:159409/1‑143 (MQ=255)                                                                                        atatTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATAAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAg                                                         <  2:95330/150‑1 (MQ=255)                                                                                                ggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGa                                                <  2:1047376/151‑1 (MQ=255)                                                                                                   ggTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTa                                             <  2:598907/151‑1 (MQ=255)                                                                                                       gTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGGCGGGTATGAGGGGGGGGGT‑G‑TTTATGGGGGTGGCGGGGG‑G‑C‑GG‑TTTTTTTTTCCGGGGTTT‑CGAAAGGTGGGATGCCATTGGCCGGACATTAGGGGCGGGGGTTTACt                                          >  1:402044/1‑150 (MQ=255)                                                                                                               gggCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCtgg                                 <  2:575142/151‑1 (MQ=255)                                                                                                               gggCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCtgg                                 <  2:33913/151‑1 (MQ=255)                                                                                                                ggCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCtggt                                <  1:943039/151‑1 (MQ=255)                                                                                                                   cATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGc                             <  1:702773/151‑1 (MQ=255)                                                                                                                    aTTCGTGACGGCATTATCGGCGGGGGCGTCGGGGATGAGGGGCTGGCT‑G‑TTTAT‑GGGGGTGGCGGGG‑G‑C‑TG‑TTTTTTTTTTCGGGGTTTTCGCAAGACGGATCGCCATTGGCCTGGCATTAGGCGCGTGGGTTAACTGGGAGGtggggg                              >  2:1002390/1‑149 (MQ=255)                                                                                                                       cGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCgg                          <  2:255341/150‑1 (MQ=255)                                                                                                                       cGTGACGGCATTATCGGCGGGGGCGGCGGGGATTAAGGGCCGGGC‑G‑GTAAT‑GGGGGTGCCCGGG‑G‑G‑GG‑GTTTTTTTTTCGGGGTTTTCGAAAAGTGGGTCGCCCTTGGCCCGGCCTTATGGGCGGGGGTTAACTGGGAGGcggtggggggg                         >  1:500673/1‑146 (MQ=255)                                                                                                                        gTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGc                        <  2:445808/151‑1 (MQ=255)                                                                                                                                      ggcggGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGGTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGc            >  2:810507/1‑149 (MQ=255)                                                                                                                                         gggTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc       <  2:624924/151‑1 (MQ=255)                                                                                                                                         gggTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc       <  1:1003307/151‑1 (MQ=255)                                                                                                                                         gggTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc       <  2:518721/151‑1 (MQ=255)                                                                                                                                          ggTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCg      <  2:266765/151‑1 (MQ=255)                                                                                                                                              cGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAAt   >  2:79823/1‑150 (MQ=255)                                                                                                                                              cGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATa  <  1:48815/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                        CGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑G‑TTAAT‑GGGGTTGCCGGGC‑G‑C‑TG‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATA  >  NC_000913/1079321‑1079612

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑