Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,234,233	0	T	A	42.2%	62.2 / 18.0	45	Y162F (TAT→TTT)	nhaB	sodium:proton antiporter
Reads supporting (aligned to +/- strand):  ref base T (20/6);  new base A (0/19);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 7.46e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTGCCGACACCGGCATGCATCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAATATGAACAGC  >  NC_000913/1234087‑1234379                                                                                                                                                    |                                                                                                                                                    cGGTGCCGACACCGGCATGCATCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATaaa                                                                                                                                                  >  2:767012/1‑150 (MQ=255)      ccGACACCGGCATGCATCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑cc                                                                                                                                             >  2:30709/1‑149 (MQ=255)         acacCGGCATGCATCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTg                                                                                                                                        >  2:357386/1‑151 (MQ=255)                catgcatCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCt                                                                                                                                 <  2:245155/151‑1 (MQ=255)                            ggCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGc                                                                                                                     <  2:593069/151‑1 (MQ=255)                              cTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGcc                                                                                                                    >  1:1630/1‑150 (MQ=255)                                 cGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCacg                                                                                                                 >  2:107213/1‑150 (MQ=255)                                 cGCAAAAAGCCACGAACCTTTCCCAGAACCACTTTGAAATGCTGGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATCCAAAAAAAA‑CCGACTGCACCGCTGATCACCACCGCCacg                                                                                                                 <  2:416828/150‑1 (MQ=255)                                      aaaGCCACGGAACTTTTCCAAAACCATTTTTTAATGCTTGTCAATATGACTATCGTCTTGCAGGTCGGTTTCTTCGGTCCGGGAAGAG‑GCTCCGCGGTAATAAATACCATAAAAA‑CCGACTGCAACGCTGATCCCCACCGCCACGACGGt                                                                                                            <  1:362571/150‑1 (MQ=255)                                      aaaCCCACGGAACTGTCCCAGACCCACTTTGAAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGAAAGAG‑GCTCCGCGGTGATAAATCCCAAAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGtt                                                                                                           <  2:711996/151‑1 (MQ=255)                                       aaGCCACGGAACTGTTCCAGAACCGTTTTGTAATGCTTGTCGATATGATTATCTTCTTGAGGGTGGGTGTCTTCGTTACGGGAAGAG‑GCTACGCGGTGATAAATCCCATAAAAC‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTa                                                                                                          <  1:658239/151‑1 (MQ=255)                                         gCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTa                                                                                                          >  1:644759/1‑149 (MQ=255)                                           cACGGAATTTTTCCAGACCCACTTTGTAAGGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTAGGGGAAGAG‑GCTACGGGGTGATAAATCCAAAAAAAA‑CCGACTGAAACGCTGATCACCACCGCCACGACGGTTaa                                                                                                         <  1:390585/148‑1 (MQ=255)                                                aaCTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCg                                                                                                  >  2:291159/1‑150 (MQ=255)                                                  cTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAgg                                                                                               >  1:781817/1‑151 (MQ=255)                                                     tcccaaacccgcTTTTTAATGCTTGTCGATATGACTATCTTTTTGCAGGTGGGTGTCTTCGGTACGGGAAGAG‑GCTCCGCGGTGATAAATACCAAAAAAC‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGaa                                                                                             <  2:29652/139‑1 (MQ=255)                                                         aGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCgg                                                                                        >  2:270948/1‑151 (MQ=255)                                                                      aaTGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATCCCAAAAAAC‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAgc                                                                           <  1:534919/151‑1 (MQ=255)                                                                      aaTGCTGGTCGATATGACTATCGTCTTGAGGATGGGTGTCTTCGTTACGGGAAGAG‑GCTACGCGGTGATAAATCCCAAAAAAA‑CCGACTGCAACACTGATCCCCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCa                                                                             <  1:324264/149‑1 (MQ=255)                                                                                  tatGTCTTTCGTCTTGGAGGTCGGTGTCTGCGGTAGGGGAAGAG‑GCTACGAGGTGATAAATCCCAAAAAAA‑CCGCCTGCAACGCTGACCCCCCCCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCaaa                                                                <  2:514561/150‑1 (MQ=255)                                                                                     gatgattgTCTGGAAGGTGGGCGTTTTCGGTA‑GGGAAAAGAGCTCCGCAGTGAAAAACACCAAAAAGC‑CCGACTGCAACGCTTTTCCCCCCCGCCACGACGGTTAAGGCATCGAGGAACGCGGGGAGTAACGCAGCCGCCACGcca                                                                 <  2:258696/139‑3 (MQ=255)                                                                                        tATCGTTTGGAAGGTGGGTGTTTCCGGTCGGGAAAGGG‑TCTCCG‑GGTTAAAAAAACCAAAAAAACCCGACGCCAACGCGGATCACCCCCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACg                                                                    <  1:569029/140‑1 (MQ=255)                                                                                        tATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAagag                                                           >  1:680788/1‑149 (MQ=255)                                                                                            gTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGAc                                                     >  1:352239/1‑151 (MQ=255)                                                                                             tCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGAc                                                     >  2:46916/1‑150 (MQ=255)                                                                                                 gCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGAcagc                                                  >  1:711100/1‑149 (MQ=255)                                                                                                    ggTCGGTGTCTTCGGTACGGAAAGGG‑GCTACGCGGTAATAAATCCAATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGAcagca                                                 <  1:116092/147‑1 (MQ=255)                                                                                                             cTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCg                                    >  1:49242/1‑151 (MQ=255)                                                                                                              ttCGGTCGGGAAAGGG‑GCTCCGGGGTAAAAATTCCCAAAAAAA‑CCGACTGCACCGCTGATCACCCCCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCg                                    <  1:196512/150‑1 (MQ=255)                                                                                                              ttCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCg                                    >  1:699253/1‑150 (MQ=255)                                                                                                                cGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAAt                                 >  1:57646/1‑151 (MQ=255)                                                                                                                cGGTACGGAAAGAG‑CCTCGGCGGTAAAAAATACCAAAAAAC‑CCGACGACACCGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAAt                                 <  2:704131/151‑1 (MQ=255)                                                                                                                 ggtgtgggAGGGG‑GCTACGGGGTGAAAAAACCCATAAAAC‑CCGCCTCCAACGCTTACCCCCTCCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAg                                      <  1:64257/140‑1 (MQ=255)                                                                                                                 ggTAGGGGAAGAG‑GCTACGGGGTGATAAATCCCAAAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGc                                     <  1:375930/146‑1 (MQ=255)                                                                                                                 ggTAGGGGAAGAG‑GCTACGCGGTGATAAATCCCAAAAAAC‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAAt                                 <  1:297101/150‑1 (MQ=255)                                                                                                                   tACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACCGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCt                              >  2:604646/1‑151 (MQ=255)                                                                                                                      gggAGGGG‑GCTACGGGGTAAAAAATCCAAAAAAAC‑CCGACTGCAACGCTGTTCCCCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCt                              <  2:423838/148‑1 (MQ=255)                                                                                                                         aaGGG‑GCTACGCGGTAAAAAATCCAAAAAAAA‑CCGACTGCACCGCGGATCCCCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAAc                          <  2:256100/149‑1 (MQ=255)                                                                                                                             g‑gCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCaa                     >  1:790386/1‑150 (MQ=255)                                                                                                                                      ggTGAAAAATCCCAAAAAAC‑CCGACTGAAACGCTGATCCCCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAAc                   <  2:660966/144‑1 (MQ=255)                                                                                                                                          aaaaaTCCCAAAAAAA‑CCGACGGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAatat         <  1:191101/148‑1 (MQ=255)                                                                                                                                          aTAAATCCCAAAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAat           <  1:125278/148‑1 (MQ=255)                                                                                                                                            aaaTCCCAAAAAAC‑CCGACTGCAACGCTGATCCCCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAat           <  1:430583/146‑1 (MQ=255)                                                                                                                                             aaTACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGAAAATATGaa      >  2:675047/1‑150 (MQ=255)                                                                                                                                                 ccATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAATATGaacagc  >  1:385922/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                    CGGTGCCGACACCGGCATGCATCATCAGGCTACGCAGAAAGCCACGGAACTGTTCCAGAACCACTTTGTAATGCTTGTCGATATGACTATCGTCTTGCAGGTCGGTGTCTTCGGTACGGGAAGAG‑GCTACGCGGTGATAAATACCATAAAAA‑CCGACTGCAACGCTGATCACCACCGCCACGACGGTTAAGGCATCGAGGAACGCGGAGAGGAACGCAGCCGCCACGCAAAAAGAGAGCGACAGCAGCATTTTGGAGCGAATGCTTAACAGCAAACGGGTAAATATGAACAGC  >  NC_000913/1234087‑1234379

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑