Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,481,804	0	G	A	43.2%	60.6 / 18.1	44	P125S (CCA→TCA)	emrY	putative multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base G (23/2);  new base A (0/19);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.49e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTT  >  NC_000913/2481658‑2481944                                                                                                                                                    |                                                                                                                                             ccAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAAt                                                                                                                                           <  2:360900/150‑1 (MQ=255)  cAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTa                                                                                                                                         <  1:3972/151‑1 (MQ=255)                        aaaTATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTg                                                                                                                   >  2:642253/1‑151 (MQ=255)                           tataACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAAc                                                                                                                >  2:709294/1‑151 (MQ=255)                                 ccccaaaTACCGGCCCACATACGGGAGCAATAACCAGGGTCATTGACCATAATGCAAGAGCAATTTTTTTTTTTTCGGGGGGATATTCCCTAAAAAATAAACTCT‑GTGACAGTGAAATTACCGCCCCCGCCATTAACCCCTGAACGActct                                                                                                          <  2:526061/146‑1 (MQ=255)                                     cAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaa                                                                                                       >  2:34042/1‑150 (MQ=255)                                      aaTATCGGCACACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaa                                                                                                      >  1:203609/1‑150 (MQ=255)                                             ccccAAATACGGGAGCGATAATCCCGGTCATTGACAATAAGGCCAAAGAAATTTTTTTTTTTTCGGGCGAATATTTCTTTAATAATAACCTCT‑GTGACAGGGAATTTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAg                                                                                              <  2:476229/150‑1 (MQ=255)                                              cccACATATCGGAGCGATAATCACGTTCATTGCCCAAAATCCAAGAGCAAATTTTTTTTTTTCTGGGGGATAATTCCTAAAAAAAAACCTCT‑GTGACAGTGAAATTAAGGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAg                                                                                              <  2:14420/150‑1 (MQ=255)                                              cccAAATATGGGAGCAATATTCCCGGTTATTGACCATAATGCAAAAAAAATTGTTCTTTTTTCGGGCGGATATTTCATAAAAAAAAAACTCT‑GTAAAAGAGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAat                                                                                                   <  1:9777/145‑1 (MQ=255)                                                 acaTATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                           >  1:388851/1‑150 (MQ=255)                                                 acaTATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                           >  2:318168/1‑150 (MQ=255)                                                   atatCGGAGCAATAATCACGGTCATTGACCATAATGCCAGAGAAAATGTTTTTTTTTCGGGGGGATAATTCCTAAATAATAATCTCG‑GTGACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                           <  2:573259/148‑1 (MQ=255)                                                                aaccACGGTCATTGACCAAAATGCAAGAAAAATTTTTTTTTTTTCGGGGGGATATTTCTTAAAAAAAAACCTCT‑GTGAAAGTGAAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGa                                                                            <  1:172439/147‑1 (MQ=255)                                                                    aCGGTCATTGACAATAATGCCAGAGCAATTTTTTTTTTTCCGGGCGAATAATTCTTTAAAAAAAACCTCT‑GTGACAGTGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAg                                                                         <  2:736689/149‑1 (MQ=255)                                                                     cGGTCATTAACAAAAACCCCAGAGCAATTTTTTTTTTTTCGGGGGAATATTTCCTAAAAAAAAACCTCT‑GTAAAAGGGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATa                                                                          <  1:770917/147‑1 (MQ=255)                                                                            tGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAtt                                                               >  2:594741/1‑151 (MQ=255)                                                                                cATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATg                                                           >  2:545866/1‑151 (MQ=255)                                                                                 aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATg                                                           >  2:650267/1‑150 (MQ=255)                                                                                   aaTCCCAGAGAAAATGTTTTTTTTTCGGGCGAATAATTCCTAAAAAAAAACCTCT‑GGGACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGaa                                                         <  2:317024/150‑1 (MQ=255)                                                                                    aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGa                                                          >  2:180011/1‑148 (MQ=255)                                                                                        cAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGc                                                   >  1:848309/1‑151 (MQ=255)                                                                                         agaaaaattttttttttttCTGGCGTATAATTCC‑TAAAAAAAAACCCTGGTAACAGTGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGa                                                       <  2:493463/133‑1 (MQ=255)                                                                                          gagCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCg                                                  >  1:6729/1‑150 (MQ=255)                                                                                            gCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaa                                                >  1:760567/1‑150 (MQ=255)                                                                                                 tttttttttttCTGGGGAATAATTCATAAAAAAAAAACTCT‑GGGAAAGTAAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaa                                            <  1:669803/144‑1 (MQ=255)                                                                                                   tttttttttGGGGGGAATAATTCCTTAAAAATAAACCCT‑GAAACAGTAAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaaa                                           <  1:130955/145‑1 (MQ=255)                                                                                                   tttttttttCTGGCGAATATTTCTTTAAAAATAAACTCT‑GGGAGAGTGAAATAAAGGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaaaa                                          <  2:326420/146‑1 (MQ=255)                                                                                                   ttCTTTTTTCGGGCATATATTTCTTAAAAAAAAAACTCT‑TTAATAGTGAATTCACCCCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaaa                                           <  2:860608/148‑1 (MQ=255)                                                                                                      ttttttCTGGCGAATAATTCTTTAAAAAAAACCTCG‑GTGAAAGTGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGt                                        <  1:31154/148‑1 (MQ=255)                                                                                                        ttttCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTg                                   >  2:785774/1‑151 (MQ=255)                                                                                                            cTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGaa                                 >  1:109458/1‑149 (MQ=255)                                                                                                                       ttCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATc                    >  2:185756/1‑151 (MQ=255)                                                                                                                        tCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCt                   >  2:238517/1‑151 (MQ=255)                                                                                                                          cTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt                  >  1:452961/1‑150 (MQ=255)                                                                                                                           ttAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTa                 >  1:721238/1‑150 (MQ=255)                                                                                                                             aaaaaaaacctct‑GTGAAAGTGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt                  <  2:453015/138‑1 (MQ=255)                                                                                                                             aaaaaaaaaCTCG‑GTGAAGGTGAATTTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaata                       <  1:642167/136‑1 (MQ=255)                                                                                                                                  taaACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCt         >  2:842139/1‑151 (MQ=255)                                                                                                                                   aaaCTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCt         >  2:81303/1‑150 (MQ=255)                                                                                                                                      ctct‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTc     >  2:37779/1‑151 (MQ=255)                                                                                                                                         t‑gtgACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCttt  >  1:338426/1‑151 (MQ=255)                                                                                                                                         t‑gtgAAAGTAAAATAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCtt   <  1:238479/150‑1 (MQ=255)                                                                                                                                           gaaaCAGTGAAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTc     <  1:194019/144‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                             CCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCT‑GTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTT  >  NC_000913/2481658‑2481944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑