Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	884,346	0	C	G	50.0%	47.2 / 10.7	36	A225G (GCG→GGG)	mdfA	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (1/17);  new base G (18/0);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 4.19e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTT  >  NC_000913/884200‑884496                                                                                                                                                   |                                                                                                                                                        gttggCCGCGTTGCCGGCGTTGTCCTTTTACGGGGTGCACGGCGCCGTCCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGggc                                                                                                                                                         <  1:797202/147‑1 (MQ=255)       cGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGgcg‑ctggcgctg                                                                                                                                              <  1:889536/151‑1 (MQ=255)        gCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGgg‑cggggggtgg                                                                                                                                             >  2:762534/1‑151 (MQ=255)            tGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGAt                                                                                                                                          <  2:619758/150‑1 (MQ=255)               cAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CCGGGGCGGGGGttgg                                                                                                                                       >  1:772312/1‑148 (MQ=255)                  cGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GGGGGGCTgggggt                                                                                                                                         >  2:446508/1‑142 (MQ=255)                    aTCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGg‑cgggggcgggggggctttagt                                                                                                                                  >  1:27968/1‑140 (MQ=255)                      ctcCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GTGGGGCGGGGGttgggttgt                                                                                                                                  >  2:600269/1‑141 (MQ=255)                                ggTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GGGGGGGCGGGGTTTGTTTGTCTGcgggtggggg                                                                                                                     >  1:926455/1‑142 (MQ=255)                                        aCGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATc                                                                                                             <  2:628581/151‑1 (MQ=255)                                              cATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GCGGGGCTGGGGGTTGTTTGTTTGCCGTTGCTgggggggggggccc                                                                                                         >  2:875467/1‑137 (MQ=255)                                                 gCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GTGGGGGTGGGGTTTGGTTGTCTGCCGTTGCCggggggggtgcccc                                                                                                         >  2:177496/1‑134 (MQ=255)                                                 gCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCg                                                                                                    <  1:368578/151‑1 (MQ=255)                                                  ccTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GGGGGGCGGGGGTTTGTTTGGCTGCCGCTGCTGGGGGGGGGCGccccctcg                                                                                                    >  2:876230/1‑145 (MQ=255)                                                    tGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CTGGGGGCGGGGTTTGTTTGGTTTCCGTTGCTGGGGGGGGGCGcccc                                                                                                        >  2:98751/1‑143 (MQ=255)                                                     gAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GGGGCGCGGGGGTGCTTTTGTGTGCCGTTGTTGGGGTggggctacccgacg                                                                                                    >  1:301524/1‑135 (MQ=255)                                                              aCGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTAtcatca                                                                                       <  1:156910/151‑1 (MQ=255)                                                                    ataGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTAcc                                                                                  <  1:586560/150‑1 (MQ=255)                                                                    ataGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCg                                                                                 <  2:487821/151‑1 (MQ=255)                                                                      aGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CCGGCGCTGGGGGTTGTTTTGCTGGCGTTGTTGGCGTGGGGCGCCCCgccgcccggtctca                                                                                          >  1:537893/1‑132 (MQ=255)                                                                                  gTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CTGGGGCTGGGGGTTGTTTGTTTGCCGTTGGTGGGGGGGGTCGCCCCCGCGCCGGTTATTTTCAtttaccgcggggcggt                                                                       >  2:370104/1‑133 (MQ=255)                                                                                   tCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CGGGGGCTGGGGGTCGGTTGGCTGCCGTTGCTGGCGGGGGGGGCCCCGGCGCCGCTTATCATCCTTTCCCGCGGGccggt                                                                       >  1:284955/1‑142 (MQ=255)                                                                                       tGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGGCGGGGGTTGGTT‑GGCTGCCGTTGGTGGGGGGGGGCGCCCCGTCGCCCCTTATCAACATTTCTGGCgcagcggtg                                                                      >  1:494641/1‑135 (MQ=255)                                                                                         acaGAACACTGTCGTGATTATAAGCTGGTGCTGAAGAACGGCCGCTGTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGGCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGTAGCTATg                                                            <  1:544555/149‑1 (MQ=255)                                                                                         aaaGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATg                                                            <  1:516951/151‑1 (MQ=255)                                                                                               cTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑GCGGGGCCGGGGTTCGTTTGTCTGCCGGTGCTGGGGGGGGTCGCCCCCGCGCCGGTTTTCATCATTTACCGCGGGCAGGTGAGGAGGTATgga                                                          >  2:616604/1‑145 (MQ=255)                                                                                               cTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CCGGGGCTGGGGTTTGTTTGTTTGCCGTTGTTGGGGGGGGTTGCCCCGGCGGCGGTTTTCATCCTTTCCcgcggg                                                                            >  2:757138/1‑127 (MQ=255)                                                                                                        gACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CTGGGGCTGGGGGTCGTTATTCTGCCGCTTCTGGCGTGGGTCGGCCCATCGCCGGATATTATCATTAACCGCGCGGAGGTGAGCAGCCATGAAAATTGCttt                                                 >  2:211472/1‑146 (MQ=255)                                                                                                                 cTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGG‑CTGGCGCCGGGGTTTGTTAGTTTGCCGGTGCTGGGGGGGGGCGCCCCGCCGCCGGCTTTTTTCATTAACCGCGCGGAGGTGAGGAGCCATGAAAATTGGTTGCTTCCAGTg                                        >  2:304017/1‑147 (MQ=255)                                                                                                                   ggTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTa                                    <  2:142973/149‑1 (MQ=255)                                                                                                                     tGCTGAAGATCGGCCTCTGTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCTGTTGCGGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCTGCGACCAGTTTAGCAGCTATGAATATGGCTTGCTGCAAGTTCTTAttt                                 <  1:726380/150‑1 (MQ=255)                                                                                                                      gCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTc                               <  1:112447/151‑1 (MQ=255)                                                                                                                          aagaaCGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCgggg                           <  1:900138/151‑1 (MQ=255)                                                                                                                             aaCGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGt                        <  2:15084/151‑1 (MQ=255)                                                                                                                                 gCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAAt                    <  1:704803/151‑1 (MQ=255)                                                                                                                                    gCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGc                 <  2:639970/151‑1 (MQ=255)                                                                                                                                           ggCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAAc          >  2:195499/1‑151 (MQ=255)                                                                                                                                              gggggCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACtt        <  2:787578/150‑1 (MQ=255)                                                                                                                                                gggCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCt     <  1:174046/151‑1 (MQ=255)                                                                                                                                                 ggcg‑ctggcgctGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTg    <  1:875481/151‑1 (MQ=255)                                                                                                                                                   cg‑ctggcgctggGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGtt  <  2:27994/151‑1 (MQ=255)                                                                                                                                                   cg‑ctggcgctggGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGtt  <  2:926467/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                        GTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCG‑CTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTT  >  NC_000913/884200‑884496

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑