Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	298,960	0	A	C	46.3%	51.0 / 15.9	42	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
Reads supporting (aligned to +/- strand):  ref base A (19/3);  new base C (0/19);  total (19/23)
Fisher's exact test for biased strand distribution p-value = 8.01e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGC  >  NC_000913/298813‑299101                                                                                                                                                        |                                                                                                                                              tataCACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATAccc                                                                                                                                            >  2:644582/1‑151 (MQ=255)  ataCACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATAcccc                                                                                                                                           >  1:769779/1‑151 (MQ=255)        cgcgTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCat                                                                                                                                      >  1:269388/1‑150 (MQ=255)         gcgTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCatat                                                                                                                                    >  2:803948/1‑151 (MQ=255)            tgggCGATACCCGCGCTCACGCCGCACAGGCCCAGCTCACCAACCCCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCACCC‑AGGAAAATCC‑CCTCCTGTTTGGGGATATCCGCATGACCCGGCCCCTCATACCCCGCCata                                                                                                                                     <  2:617166/145‑1 (MQ=255)             tGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTg                                                                                                                                >  1:10540/1‑151 (MQ=255)                cGATAGCCGCGCTCACGCCGCACAGGCCCAGCCCCCCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATAGGGGGTCGGTATCACCC‑AGGAAAATCC‑CCCCCTGTTTGGGGATACCCGCATGAACCGGCCCCTCATCCCCCGCCATATCGTGAtt                                                                                                                             <  1:512855/151‑1 (MQ=255)                        gcgcTCACCCCGCACAGGCCCATCTCCCCGACCCCTTGGG‑CCTTCA‑TCGGGGAGAATAGGGGGTCGGTATCATCC‑GGAAAAATCC‑CCTCCTGTTTTGGGATAACCGCAGGAACCGCCGCCTCATCCCCCGCCATATCGTGATTAACGa                                                                                                                        <  1:758587/148‑1 (MQ=255)                         cgcTCCCGCCGCACAGGCCCAGCCCCCCGACACCTTGGC‑CCTTCA‑TGGGGGAGGATATGGGGTCGGTACCACCC‑AGAAAAACCC‑CCTCCTTTTTGGGAATACCCAAAGGACCGGCCCCCTCATCCCCCGCCATATCGTGATTAACGaa                                                                                                                       <  2:189975/148‑1 (MQ=255)                             cccgccgcACAGGCCCAGCTCACCGCCCCCTTTGG‑CCTTCA‑TGGGGGAGGATATGGGGTCGGTATCACCC‑AGAAAAATCC‑CCTCCTTTTTTGGAATATCCGCATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAg                                                                                                                   <  1:392074/146‑1 (MQ=255)                             cACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGccc                                                                                                                >  2:806588/1‑151 (MQ=255)                               cgccgcACAGCCCCAGCTCCCCGACCCCTTTGG‑CCTTCA‑TGGGGGAGGATATGGGGTCGGTATCACCC‑AGAAAAATCC‑CCTCCTGTTTGGGGATACCCGCATGAACCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGcc                                                                                                                 <  1:331567/148‑1 (MQ=255)                                gccgcACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCaa                                                                                                              >  1:550625/1‑150 (MQ=255)                                     acaGGCCCAGCTCACCGACCCCTTTGC‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCACCC‑AGAAAAACCC‑CCTCCTGTTTTGGGATATCCGCATGACCCGGCCCCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGt                                                                                                         <  1:307456/150‑1 (MQ=255)                                       agccccAGCTCACCGACCCCTTTGG‑CCTTCA‑TCGGGGAGGATAGGGGGTCGGTATCATCC‑AGGAAAATCC‑CCTCCTGTTTGGGGATACCCGCATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCa                                                                                                       <  1:271572/147‑1 (MQ=255)                                               cccACCGAC‑CCTGTTG‑GCTTCACTCGGGGAGGATA‑GGGGGCGGTAACCGCCAAGAAAAATCA‑CCTCGTGTTTGGGAATATCGCCAGGACCCGGCCCCCCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGcc                                                                                              <  2:815208/149‑1 (MQ=255)                                               cTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGCATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGcc                                                                                              >  2:105644/1‑151 (MQ=255)                                                   ccgccccttttGC‑CTTTCA‑GGGGGGAGAATTTGGGGTCGTTATCACCA‑AGAAAAACCC‑CCTCCTTTTTGGGGATACCCCCATAACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGc                                                                                           <  1:735897/142‑1 (MQ=255)                                                       ccccTTTGGCCCTTCG‑TCGGGGAGGATATGGGGTCGGTATCACCC‑AGAAAACCCC‑CCTCCTGTTTTGGAATACCCGAATAAACCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCGCCGCCAg                                                                                            <  2:662977/144‑1 (MQ=255)                                                                 ccTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGc                                                                             >  1:699350/1‑151 (MQ=255)                                                                  cTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGcc                                                                            >  1:176444/1‑151 (MQ=255)                                                                     cA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCcgcg                                                                         >  1:338639/1‑151 (MQ=255)                                                                      a‑TCGGGGAGGATAGGGGGCCGGTCACACCC‑AAAAAAACCC‑CCTCCTTTTTTGGATTACCCCAATAACCCGCCCCCTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGcc                                                                            <  2:60017/147‑1 (MQ=255)                                                                             gaggaTATGGGGTCGGAATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATAGACGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAAAGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTGCATCAGTGCCGCgcccatg                                                                   >  2:271587/1‑150 (MQ=255)                                                                                     ggtgcctgTATCATCC‑AGTAAACCCC‑CCCCTTGTGGGGGGATAGCCGAGTAGCCCGCCCCCGCATGCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCgcccatgcccat                                                              <  2:834400/140‑1 (MQ=255)                                                                                     ggggTGGGTATCACCC‑AGAAAAACCC‑CCTCCTTTTTTGGGATACCCGCATGACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTc                                                          <  1:792071/151‑1 (MQ=255)                                                                                     ggggTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTc                                                          >  2:578840/1‑151 (MQ=255)                                                                                     ggggTCGGTATCACCA‑AGAAAAATCC‑CCCCCTGTTTGGGGATACCCGCATGACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATa                                                             <  1:447727/148‑1 (MQ=255)                                                                                           ttgttatccccgagAAAATCACCCTATTTTTTAGGGAAATCCCCCCGACCCGGCCCTCCAAACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCAtt                                                       <  1:434675/137‑1 (MQ=255)                                                                                            gTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTgcgc                                                   >  2:6360/1‑151 (MQ=255)                                                                                                  tcC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGCAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGcc                                                  >  2:256578/1‑146 (MQ=255)                                                                                                  ccc‑AGAAAAATCC‑CCTCTTTTTTTGGGATATCCGCATAACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCa                                                 <  2:48534/146‑1 (MQ=255)                                                                                                      agaaaaaCCC‑CCCCCTGTTTGGGGATACCCGAATGACCCGGCACCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGcc                                                  <  1:308852/140‑1 (MQ=255)                                                                                                      aGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCt                                          >  2:60549/1‑151 (MQ=255)                                                                                                               cccctcctGTTTGGGGATCCCCGCATGACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTg                                     <  1:90722/146‑1 (MQ=255)                                                                                                               ccccccctTTTTGGGGATACCCGAATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTgc                                    <  1:680581/144‑1 (MQ=255)                                                                                                                        tttgGGGATCTCCGAATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGtt                            <  1:671881/148‑1 (MQ=255)                                                                                                                         tttGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCg                        >  1:362864/1‑151 (MQ=255)                                                                                                                                          aaCCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAACCGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACATGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTcc        >  2:584183/1‑150 (MQ=255)                                                                                                                                                ccccTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTgca    <  1:193506/146‑1 (MQ=255)                                                                                                                                                cACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTgcagc  >  2:34575/1‑150 (MQ=255)                                                                                                                                                  ccTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTgcagc  <  1:825223/148‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                              TATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCA‑TCGGGGAGGATATGGGGTCGGTATCATCC‑AGGAAAATCA‑CCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGC  >  NC_000913/298813‑299101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑