Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,079,468	0	A	G	44.4%	46.5 / 10.2	36	D55G (GAT→GGT)	putP	proline:sodium symporter
Reads supporting (aligned to +/- strand):  ref base A (5/15);  new base G (16/0);  total (21/15)
Fisher's exact test for biased strand distribution p-value = 3.22e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATACAACA  >  NC_000913/1079347‑1079617                                                                                                                          |                                                                                                                                                            atCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGTTGGGTATGA‑GGGGGTGGC‑T‑GGTTAT‑gggggt                                                                                                                              >  1:723234/1‑147 (MQ=255)   cTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGA‑GCGGCGGGC‑C‑GTTTAT‑gggg                                                                                                                                >  1:330213/1‑145 (MQ=255)           tGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGATTA‑GCGGGTGGC‑T‑GGTTAT‑GGGGGTGGCggg                                                                                                                        >  2:774264/1‑145 (MQ=255)            gATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTCGGGGATGA‑GGGGGGGGG‑TGGTTATT‑GGGGTGGCggggg                                                                                                                       >  2:309790/1‑145 (MQ=255)             atatTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGGTATGA‑GAGGCCGGG‑TGGTTATT‑GGGGTGGCgggggccgtgt                                                                                                                 >  2:790082/1‑144 (MQ=255)                 tgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGATGA‑GGGGCTGGCGG‑GTTATT‑GGGGTGGCGGGGGGGG‑G‑ttttt                                                                                                            >  2:746897/1‑150 (MQ=255)                      gggTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGGGTGG‑GGGGGCGGC‑C‑GGTCTT‑AGGGGTGCCGGGGGCT‑G‑Tttttttttt                                                                                                       >  2:649894/1‑148 (MQ=255)                                  tGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGG‑GGGGGGGGG‑G‑GTTTAT‑TGGGGTGGCGGGGGGT‑G‑GTTTTTTTTTCGGGGTTTTCGaa                                                                                          >  1:367767/1‑150 (MQ=255)                                     cGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCt                                                                                      <  2:503845/151‑1 (MQ=255)                                         cAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGAt                                                                                  <  1:123038/151‑1 (MQ=255)                                         cAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGAt                                                                                  <  1:189010/151‑1 (MQ=255)                                          aaCGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATc                                                                                 <  1:732508/151‑1 (MQ=255)                                             gAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTTTGT‑GGGGGGGGG‑G‑GTTTATGGGGGTGGCGGGGGGCG‑G‑TTTTTTTTTCCGGGGTTTcgaaaaatgggaggcc                                                                               >  2:87290/1‑136 (MQ=255)                                                   cTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGGCGGGGATGA‑GGGGGGGGG‑T‑GTTTAT‑TGGGGTGCCGGGGGCT‑G‑TTTTTTTTTTCGGGGTTTTCGAAAACTgg                                                                                    >  1:19590/1‑139 (MQ=255)                                                      tGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCt                                                                      <  2:487692/150‑1 (MQ=255)                                                      tGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATTA‑GGGGGGGGG‑T‑GTTTAT‑GGGGGTGGCGGGGGCT‑G‑TTTTTTTTTTCGGGGGTTTCCAAAACTGGGTCggcctt                                                                           >  1:662150/1‑140 (MQ=255)                                                        acgacTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGTGGGGGATGA‑GGGGGTGGG‑T‑GTTAAT‑GGGGGTGGCGGGGGCG‑G‑GTTTTTTTTTCGGGAGTTCCGAAAGCTGGGACGCCATTGGCCTggc                                                                   >  2:705589/1‑149 (MQ=255)                                                         cgacTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACa                                                                  <  1:27338/151‑1 (MQ=255)                                                             tataTTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATTAGGGGGCGGGT‑G‑GTTATA‑GGGGTGGCGGGGGGCG‑T‑TTTTTTTTTTGGGGGTTTCTGAAAG‑TGGGTCGcccctgggccggcctt                                                                >  2:61910/1‑135 (MQ=255)                                                                   cTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGG‑GCGGGGGGG‑T‑GGTTAT‑GGGGGTGGCGGGGGCG‑GTTTTTTTTTTTCGGGGTTTCCGAAA‑CTGGGTTGCCACTGGGCTGGCAATatgg                                                            >  2:646887/1‑144 (MQ=255)                                                                     gggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGcgcg                                                         <  2:576933/148‑1 (MQ=255)                                                                     gggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGt                                                        <  1:228797/149‑1 (MQ=255)                                                                               aGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTgg                                             <  1:696784/150‑1 (MQ=255)                                                                                   ttGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGA‑GGGGCTGGC‑T‑GTTTAT‑GGGGGTGCCGGGGGCTGG‑TTTTTTTTTCCGGGGTTT‑CGCAAGACGGGTCGCCCCTTGCCCGACATTAAGCGCggggggttaattgga                                           >  1:551467/1‑137 (MQ=255)                                                                                          aTTCGTGACGGCATTATCGGCGGGTGCGGCGGGTATGA‑GCGGGGGGG‑T‑GTTTAT‑GGGGGTGCCGGGGGCT‑G‑TTTTTTTTTTCGGGGTTTTCGGAAGCTGGGTCGCCCCTTGCCTGACAATAGGGGCGGGGGTTAAATGGAAGCtggggg                                   >  1:448353/1‑149 (MQ=255)                                                                                            tCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGcc                                 <  1:20127/149‑1 (MQ=255)                                                                                                        tATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCgtg                    <  1:309793/150‑1 (MQ=255)                                                                                                          tCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTTCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGtgtg                  >  2:607706/1‑150 (MQ=255)                                                                                                           cggcggGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGc                 <  2:222324/150‑1 (MQ=255)                                                                                                            ggcggGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCAt               >  1:582886/1‑151 (MQ=255)                                                                                                            ggcggGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCAt               <  1:120168/151‑1 (MQ=255)                                                                                                               gggTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc            >  1:505968/1‑151 (MQ=255)                                                                                                                 gTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGa          <  2:751283/151‑1 (MQ=255)                                                                                                                      tCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATac      >  2:158753/1‑150 (MQ=255)                                                                                                                        ggATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATacaac   >  2:289543/1‑151 (MQ=255)                                                                                                                         gATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATacaaca  <  2:163671/151‑1 (MQ=255)                                                                                                                          |                                                                                                                                                            ATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGA‑GCGGCTGGC‑T‑GTTAAT‑GGGGTTGCCGGGCGCT‑G‑TTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATACAACA  >  NC_000913/1079347‑1079617

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: ‑