Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,332,823	0	A	G	50.0%	48.5 / 17.5	53	pseudogene (1580/4605 nt)	yfaS	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base A (5/21);  new base G (26/0);  total (32/21)
Fisher's exact test for biased strand distribution p-value = 6.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTAC  >  NC_000913/2332675‑2332968                                                                                                                                                      |                                                                                                                                                   gcTATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTAACGGCGGC‑GGGgaga                                                                                                                                                  >  2:723127/1‑151 (MQ=255)  cTATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGAt                                                                                                                                                 >  2:593005/1‑151 (MQ=255)  cTATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCCCGGGTTATCGGCGGC‑GGGgggag                                                                                                                                                 >  1:622265/1‑150 (MQ=255)    aTTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTTTCGGGGGC‑GGGGGGActt                                                                                                                                               >  1:527430/1‑151 (MQ=255)    aTTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGttt                                                                                                                                               >  1:259453/1‑151 (MQ=255)     ttACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGAattt                                                                                                                                              >  1:461126/1‑150 (MQ=255)     ttACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTa                                                                                                                                              >  2:22642/1‑151 (MQ=255)       aCTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTaa                                                                                                                                             >  2:550877/1‑150 (MQ=255)          gTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTAGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTaaacc                                                                                                                                          >  1:653042/1‑147 (MQ=255)                      ggTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGGTTTACGCCACAttaacggcg                                                                                                                             >  1:808609/2‑143 (MQ=255)                       gTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTTACCCCCCATGAcctgg                                                                                                                              >  2:766636/1‑146 (MQ=255)                       gTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGAc                                                                                                                                  <  1:766270/145‑1 (MQ=255)                        tACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACCCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTTTCGGCGGC‑GGGGGGCTTTAACGCCACCTCAccccagc                                                                                                                            >  2:729325/1‑145 (MQ=255)                         aCTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTAAGCCACATGACCGCCGGCg                                                                                                                          >  2:355944/1‑151 (MQ=255)                                  gTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTTACCCCCCCAGACCCCTGGCGTCGGgcac                                                                                                                  >  2:153090/1‑150 (MQ=255)                                  gTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCCCATGACCGCTGGCGTCGGacac                                                                                                                  >  2:784538/1‑150 (MQ=255)                                       gcgcCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTTACGCCAAATCACCCCCCGCGTCGGGCCCCGttt                                                                                                             >  1:69909/1‑150 (MQ=255)                                       gcgcCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTTAAGCCCCCTGACCGCCTGCCCCGGGCACCGtttt                                                                                                            >  2:500034/1‑150 (MQ=255)                                          ccAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGc                                                                                                          <  1:519096/150‑1 (MQ=255)                                                  cgTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGAATTAAAGCCACAAGACCGCTGGGGGCGGGCACCGTTTCGCTG‑cccttca                                                                                                >  2:347771/1‑146 (MQ=255)                                                        aTGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATGACCGCTGGGGTCGGGACCCCTTTCCCTG‑CCTTCCCGCGaca                                                                                          >  2:272405/1‑151 (MQ=255)                                                             gATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGCGATTTAACGCCCCCAGACCCCTGGCGTCGGGAACCGTTTCGCCG‑CCTTCCAGCGCCACcggg                                                                                     >  2:417843/1‑151 (MQ=255)                                                              aTCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCGCTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGa                                                                                    <  1:502903/151‑1 (MQ=255)                                                               tctcTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGCGGGGGGGATTTAA‑GCCACAATACCCCTGGCGTCCGGCACCGTTTCGCTG‑CCTTCCcgcgcaaccgggga                                                                                   >  1:31111/1‑141 (MQ=255)                                                               tctcTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGAATTAAAGCCACATGAACGCCGGGCGCGGGCACCCTCTCGCTGCCCTTCCA‑CGACACggggga                                                                                   >  1:223450/1‑149 (MQ=255)                                                                ctctTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCCCATGACCGCTGGCGTCGGACACCCTTTCGCTG‑CCTTCCCGCGACACGGGGaaa                                                                                  >  2:491018/1‑151 (MQ=255)                                                                  ctTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAACGCCCCATGAACGCCGGGGGCCGACACCGTTTTGCCG‑GCTTCCCGCCACCCGGGGgaaaa                                                                                >  2:261062/1‑149 (MQ=255)                                                                  ctTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATTACCCCCGGCGTCGGGCACCCTTTCGCTG‑CCCTCCAGCGAAACGGGGGAACg                                                                                >  2:1579/1‑151 (MQ=255)                                                                    ttGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTc                                                                              <  2:808699/151‑1 (MQ=255)                                                                          gtggtgACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTAAGCCACCTGACCGCTGGCGTCGGGAACCGTTTTCCTG‑CCCTCCAGCGACCCGGGGAAAAGGCCGGGAt                                                                        >  2:679093/1‑151 (MQ=255)                                                                           tggtgACGCGATACGCCGAGCCGTCATTTGCGGAGACGGTTGTCAATTAGCGGCTCGGTTTGTCGGTCGC‑GGGTAGGTTTAACGCCGCATGGCCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCTACACGGGGAAAGGTCCGGCAt                                                                        <  1:102770/150‑1 (MQ=255)                                                                                aCGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGc                                                                   <  2:69919/150‑1 (MQ=255)                                                                                aCGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGc                                                                   <  1:550621/150‑1 (MQ=255)                                                                                aCGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGc                                                                   <  2:394121/150‑1 (MQ=255)                                                                                 cgcgATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAACCCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAAAGGCCGGCATAACGCaa                                                                 >  2:466749/1‑151 (MQ=255)                                                                                               ccgTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTACGCCACATGAACGCCGGCGTCGGACACCGTTTCGCTG‑CCTTCCCGCGACCCGGGGGAAAGGCCGGCATAAAGCAAAACGTTTCCGAcc                                                    >  1:134569/1‑150 (MQ=255)                                                                                                 gTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAAAGCCACATTACCGCTGGCGTCGGACACCGGTTCGCTG‑CCTTCCAGCCACACGGGGAAACGGCCGGCATAACCCCAATTGTTACCCACCCtt                                                 >  2:787333/1‑151 (MQ=255)                                                                                                   cACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAACGCCACATGACCGCCGGCGTCCGAAACCGTTTCGCTG‑CCTTCCAGCCACACGGGGGAACGTCCGGCATAACCCAAATCGCTACCGGCCAttta                                               >  1:90008/1‑149 (MQ=255)                                                                                                    aCTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGAt                                              <  1:347594/151‑1 (MQ=255)                                                                                                     cTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATa                                             <  2:461357/151‑1 (MQ=255)                                                                                                     cTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATa                                             <  1:145656/151‑1 (MQ=255)                                                                                                     cTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATa                                             <  2:134595/151‑1 (MQ=255)                                                                                                     cTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCCCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTtata                                             >  2:449066/1‑151 (MQ=255)                                                                                                        gCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGGAACGTCCGGCATAACGCAAATCGTTACCCACCATTGATAAtt                                          >  2:671283/1‑151 (MQ=255)                                                                                                        gCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAAt                                           <  1:607655/150‑1 (MQ=255)                                                                                                        gCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAAt                                           <  2:805540/150‑1 (MQ=255)                                                                                                           gagaCGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGc                                        <  1:156636/150‑1 (MQ=255)                                                                                                              aCGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTg                                      <  2:79014/149‑1 (MQ=255)                                                                                                                 gTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAAAGCCACATGACCGCTGGCGTCGGGCACCGTTTCGCTG‑CCTTCCATCGAAACGGGGAAACGGCCGGCATAACGCAAACTGTTTCCCACCATTGATAATTGCttggcgg                                 >  1:8515/1‑145 (MQ=255)                                                                                                                             cGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACt                     <  1:367989/151‑1 (MQ=255)                                                                                                                               gCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTg                    <  2:627482/150‑1 (MQ=255)                                                                                                                                    gTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCAcgcg              >  2:201790/1‑151 (MQ=255)                                                                                                                                     tttATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCgg             <  1:763615/151‑1 (MQ=255)                                                                                                                                             cggc‑ggGGAGATTTAACGCCGCATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCAttttt     <  1:93798/151‑1 (MQ=255)                                                                                                                                                  ccggAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTAc  <  2:499660/148‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   GCTATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGCTGGCGTCGGACACCGTTTCGCTG‑CCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTAC  >  NC_000913/2332675‑2332968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑