Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,079,468	0	A	G	58.3%	4.7 / 23.8	24	D55G (GAT→GGT)	putP	proline:sodium symporter
Reads supporting (aligned to +/- strand):  ref base A (2/8);  new base G (14/0);  total (16/8)
Fisher's exact test for biased strand distribution p-value = 6.12e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-05

CCGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATAC  >  NC_000913/1079320‑1079613                                                                                                                                                     |                                                                                                                                                    ccGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGata                                                                                                                                                   <  1:407214/151‑1 (MQ=255)              cATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGGCGGGTATGAGGgggtgggg                                                                                                                                      >  2:461254/1‑149 (MQ=255)                      gtCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGCGGGTGGCT‑GTTTAttg                                                                                                                             >  2:232718/1‑149 (MQ=255)                        cTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATgggg                                                                                                                           <  1:6924/151‑1 (MQ=255)                              cTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGGTATGAGCGGCTGGCT‑GTTTATGGGGGTGCC‑g                                                                                                                    >  2:351744/1‑151 (MQ=255)                                     aTGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTg                                                                                                             <  1:101003/151‑1 (MQ=255)                                          attgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGCGGCTGGCT‑GTTTATTGGGGTGCC‑GGGGGCCGgtttt                                                                                                        >  2:172146/1‑151 (MQ=255)                                            tgattgGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATGAGCGGCTGGCT‑GTTTATGGGGGTGGC‑GGGGGCTGttttttt                                                                                                      >  2:515640/1‑149 (MQ=255)                                                  ggTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGTATTGGGGGCGGGGT‑GGTTATGGGGGTGGC‑GGGGGGTGGTTTTTTTTTCgg                                                                                                >  1:692949/1‑151 (MQ=255)                                                   gTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCCGGTCTGGGGGGCGGGGTGGTTATGGGGGTTGCG‑GGGGGCGGTTTTT‑TTTcc                                                                                                  >  1:573619/1‑148 (MQ=255)                                                                    cAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGGGGCGGGGATGTGGGGGTGGGT‑GTTTATTGGGGTGCCGGGGGGCGGTTTTTTTTTCTGGGGttttgtaaagtgggg                                                                               >  1:406533/1‑139 (MQ=255)                                                                                      acTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGGGGCGGGTATGAGCGGGTGGGT‑GTTTATGGGGGTGCC‑GGGGGCTGTTTTTTTTTTCGGGGGTTTCGAAAACTGGATCGCCATTGGCCTGACAtt                                                            >  2:654165/1‑151 (MQ=255)                                                                                      acTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGGTATTAGGGGCGGGGT‑GTTTATTGGGGTGGC‑GGGGGCTGTTTTTTTTTTCGGGGTTTTCGAAAGCTGGATCGCCCTTGGCCTGGCAtt                                                            >  2:260322/1‑151 (MQ=255)                                                                                           atTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGgcg                                                       <  1:530950/151‑1 (MQ=255)                                                                                                 ggCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGGCGGGTATTTGGGGGTTGGC‑GTTCATTGGGGTGCC‑CGGCGCTGTTTTTTTTTTCCGGGTTTCCGCAAGCCTGATCGCCAATGGGCTGTGATTCTGCGCggggg                                                 >  1:486295/1‑150 (MQ=255)                                                                                                    ggTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGATGCGTCGGGGAGGAGGGGGGGGCG‑GTTTAATGGGTTTCC‑GGGCGCTGTTTTTTTTTTCGGGATTTTCGAAAGCTGGGTTGCCGGTTGCCTGGCAATAGGGGGGTGGGttt                                              >  2:123539/1‑150 (MQ=255)                                                                                                     gTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGGGCGTCGGGTATGAGGGGGTGGCT‑GTTTATGGGGGTGGC‑GGGGGCTGTTTTTTTTTTCCGGGTTTTCGAAAGCTGGATCGCCCATGGGCCGACATTTGGGGCGGGGGTTaa                                             >  2:50469/1‑151 (MQ=255)                                                                                                           gTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGGTATGAGGGGCTGGGT‑GTTATTGGGGGTGGC‑GGGGGCTGTTTTTTTTTTCGGGGTTTTTGGAAGCTGGGGTGCCCTTGGCCTGGCATTTGGGGCGGGGGGTAACTgggg                                       >  1:530151/1‑149 (MQ=255)                                                                                                                                     tCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGc             <  2:672864/151‑1 (MQ=255)                                                                                                                                        gcggGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCAt           <  2:34000/150‑1 (MQ=255)                                                                                                                                        gcggGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGGTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGGTTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATa          >  1:583459/1‑151 (MQ=255)                                                                                                                                           ggTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATAcc        <  2:322557/150‑1 (MQ=255)                                                                                                                                           ggTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCg       >  2:331540/1‑151 (MQ=255)                                                                                                                                            gTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCg       <  2:152365/150‑1 (MQ=255)                                                                                                                                                 tCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGGGCATACCGAATac  <  1:538505/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CCGATGTTGGTGACATTTTGTGTCTATATCTTTGGCATGATATTGATTGGGTTTATCGCCTGGCGATCAACGAAAAACTTTGACGACTATATTCTGGGCGGTCGTAGTCTTGGGCCATTCGTGACGGCATTATCGGCGGGTGCGTCGGATATGAGCGGCTGGCT‑GTTAATGGGGTTGCC‑GGGCGCTGTTTTTCTTTCCGGGATTTCCGAAAGCTGGATCGCCATTGGCCTGACATTAGGCGCGTGGATTAACTGGAAGCTGGTGGCCGGGCGGTTGCGTGTGCATACCGAATAC  >  NC_000913/1079320‑1079613

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑