Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,079,468	0	A	G	41.9%	55.8 / 12.8	43	D55G (GAT→GGT)	putP	proline:sodium symporter
Reads supporting (aligned to +/- strand):  ref base A (4/21);  new base G (18/0);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.42e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACC  >  NC_000913/1079323‑1079607                                                                                                                                                  |                                                                                                                                                 aTGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATACGa                                                                                                                                             <  2:936121/151‑1 (MQ=255)    ttGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTCGGGTATGAggg                                                                                                                                          >  1:711275/1‑149 (MQ=255)     tGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGAGGGGCGGGTATTAGC‑gg                                                                                                                                        >  1:704177/1‑151 (MQ=255)     tGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTATATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑g                                                                                                                                         <  1:530878/150‑1 (MQ=255)              tttGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑Gt                                                                                                                               <  1:810792/150‑1 (MQ=255)               ttGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑Gtt                                                                                                                              <  1:155854/150‑1 (MQ=255)                   gtCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATgg                                                                                                                         <  1:633956/151‑1 (MQ=255)                       atatCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATgggg                                                                                                                       <  2:384192/149‑1 (MQ=255)                         atCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAGG‑GGGTGGCT‑GGTGATggggg                                                                                                                      >  2:249019/1‑147 (MQ=255)                            tttGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGGCGGGTATGAGC‑GGCGGGGT‑GTTTATtggg                                                                                                                       >  2:221629/1‑144 (MQ=255)                             ttGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCg                                                                                                                 <  1:418146/149‑1 (MQ=255)                                  aTGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATTAGG‑GGGTGGGC‑GTTTATGGGGGTGGCggggg                                                                                                             >  2:810809/1‑146 (MQ=255)                                   tGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGAGC‑GGGTGGGT‑GTTTATggggggggcggggg                                                                                                             >  1:424974/1‑137 (MQ=255)                                       attgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGG‑GGGCGGCG‑GTTTATTGGGGTGGCGGGG‑GCG‑G‑gtttt                                                                                                  >  1:1062389/1‑151 (MQ=255)                                              gggTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGCGGGGCAGGAGTTGCGT‑CGCTGGGC‑GGTCATTCGGGTGCCGGGC‑GCG‑G‑Tctttcttt                                                                                              >  2:1064791/1‑148 (MQ=255)                                                  ttATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTTTGAGC‑GGCTGGCG‑GTGTATTGGGGTGCGGGGG‑GGC‑G‑Ttttttttttttggg                                                                                        >  2:943848/1‑144 (MQ=255)                                                    aTCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGAttt                                                                                     <  2:363617/151‑1 (MQ=255)                                                    aTCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGAtt                                                                                      <  1:433481/150‑1 (MQ=255)                                                    aTCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGAtt                                                                                      <  2:1064346/150‑1 (MQ=255)                                                      cGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGGGCGGATATGAGC‑GGGCGGCT‑GTTTATAGGGGTGGCGGGG‑GGG‑G‑TTTTTTTTTCCCGGGtttt                                                                                    >  1:850699/1‑149 (MQ=255)                                                       gCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGGGCGGGGATTAGC‑GGGGGGGC‑GGTTTTGGGGGTGCCGGGG‑GCTGG‑TTTTTTTTTCTGGGTTTTcg                                                                                   >  1:95273/1‑150 (MQ=255)                                                        ccTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGTTTAGG‑GGCGGGGG‑GGTAATGGGGGTGCCGGGC‑GCC‑GTTTTTTTTTTCCGGGtttt                                                                                     >  2:377873/1‑148 (MQ=255)                                                          tGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAGC‑GGGGGGGG‑GGTTATGGGGGTGGCGGGG‑GGG‑G‑GTTTTTTTTTCgggggtt                                                                                     >  1:115641/1‑141 (MQ=255)                                                           ggCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCCTTCGGGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGaa                                                                                <  2:640641/149‑1 (MQ=255)                                                              gATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCt                                                                            <  2:758758/150‑1 (MQ=255)                                                              gATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTg                                                                           <  2:853800/151‑1 (MQ=255)                                                                 cAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGAt                                                                        <  2:29617/151‑1 (MQ=255)                                                                    cGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGGTCGGGTATGGGC‑GGCGGGGT‑GGTTATGGGGGTGCCGGGG‑GCC‑G‑TTTTTTTTTTCGGGGTTTTCGGAAGCTggggg                                                                       >  2:476315/1‑146 (MQ=255)                                                                     gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAGC‑GGCTGGGTGGTTATTGGGGTGGCGGGGG‑GCG‑G‑TTTTTTTTTCGGGGGTTTCC‑AAAGGTGGGTCGcc                                                                    >  2:158240/1‑151 (MQ=255)                                                                     gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGTCGGATATGAGG‑GGGTGGGT‑GTTTATGGGGGTGGCGGGG‑GCG‑G‑TTTTTTTTTTCGGGGTTTTCGAAAACTGGGTGGcc                                                                    >  1:124075/1‑151 (MQ=255)                                                                     gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGTTGAGCGGGCGGGTG‑GTTATTGGGGTGGCGGGGG‑GGG‑T‑TTTTTTTTTCTGGGTTTTTCTAAA‑CTGGGTCg                                                                      >  2:587650/1‑149 (MQ=255)                                                                      aaaaaCTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCa                                                                   <  1:1128143/151‑1 (MQ=255)                                                                               gacgacTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGa                                                          <  1:841454/151‑1 (MQ=255)                                                                                 cgacTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGC‑GGGTGGCT‑GTTTATGGGGGTGTCGGGG‑GCC‑G‑TTTTTTTTTTCGGGGTTTTCGAAAACTGGAGCGCCATTGGGCTggc                                                         >  1:189756/1‑148 (MQ=255)                                                                                        atTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGgc                                                  <  2:675572/150‑1 (MQ=255)                                                                                               gCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATGAGG‑GGCGGGGT‑GGTTATGGGGGTGGCGGGCGGCG‑T‑TTTTTTTTTCCGGGTTTTCC‑AAAACTGGATCGCCCCTGGCCCGGCATTTGgcggggggg                                           >  1:6487/1‑144 (MQ=255)                                                                                                 ggTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGAGC‑GGGGGGGT‑GGTTATGGGGGTGTCGGGG‑GCC‑G‑TTTTTTTTTTCGGGGTTTTCGAAAGGTGGGTCGCCATTGGCCTGACCtttagggcgggggt                                          >  1:283385/1‑137 (MQ=255)                                                                                                              ggCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCtggt                           <  1:857971/151‑1 (MQ=255)                                                                                                                     cGTGACGGCATTATCGGCGGGGGGGTCGGGTATGAGC‑GGCCGGCT‑GTTTATTGGGGTGGCGGGG‑GGG‑G‑TTTTTTTTTTCGGGGGTTTCGAAAAGTGGGGCGCCCCTGGGCTGTCCTTAGGGGCGGGGGTTAACTGGAAGCTGGGGGGCggg                    >  2:274839/1‑151 (MQ=255)                                                                                                                         aCGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGt                <  2:664727/151‑1 (MQ=255)                                                                                                                           ggCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTg              <  2:1053755/151‑1 (MQ=255)                                                                                                                                   cggcggGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGc       <  2:592903/150‑1 (MQ=255)                                                                                                                                       gggTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc  >  1:1407/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                 ATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGC‑GGCTGGCT‑GTTAATGGGGTTGCCGGGC‑GCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACC  >  NC_000913/1079323‑1079607

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: ‑