Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,332,823	0	A	G	58.3%	15.9 / 50.2	48	pseudogene (1580/4605 nt)	yfaS	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base A (7/13);  new base G (28/0);  total (35/13)
Fisher's exact test for biased strand distribution p-value = 4.02e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.23e-05

ATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTA  >  NC_000913/2332678‑2332967                                                                                                                                                   |                                                                                                                                                   aTTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGgagggtt                                                                                                                                               >  2:441801/1‑147 (MQ=255)  ttACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGtttt                                                                                                                                              >  2:544706/1‑150 (MQ=255)  ttACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTa                                                                                                                                              >  2:195520/1‑151 (MQ=255)  ttACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGAGTTa                                                                                                                                              >  2:434314/1‑151 (MQ=255)    aCTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAAc                                                                                                                                            <  1:780973/151‑1 (MQ=255)    aCTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGGTTATCGGCGGCGGGGGGGATTTaa                                                                                                                                             >  1:392329/1‑151 (MQ=255)      tGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGc                                                                                                                                          <  1:945507/151‑1 (MQ=255)       gTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAACGc                                                                                                                                          >  1:704351/1‑150 (MQ=255)       gTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑CGGGGGGTTTTACGc                                                                                                                                          >  1:648179/1‑150 (MQ=255)         aTTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGGTTATCGGCGGCGGGGGGGATTTAAccca                                                                                                                                         >  2:479412/1‑147 (MQ=255)                 gCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTTACCCCCCATGACCg                                                                                                                                >  2:675473/1‑150 (MQ=255)                 gCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGGTTAACGCCAAATGAACg                                                                                                                                >  2:796133/1‑150 (MQ=255)                 gCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGGTTATCGGCGGC‑GGGGGGGTTTTACGCCACAAGACCg                                                                                                                                >  2:1035893/1‑150 (MQ=255)                    gTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTACGCCCCATGACCCC‑Tgg                                                                                                                           >  2:799775/1‑151 (MQ=255)                    gTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAAAGCCACAAGACCGC‑Tgg                                                                                                                           >  2:548463/1‑151 (MQ=255)                    gTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGGTTATCGGCGGC‑GGGGAGATTTTACGCCAAATTACCCC‑Tgg                                                                                                                           >  2:996498/1‑151 (MQ=255)                      aCTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAAAGCCACATGACCGC‑ttggg                                                                                                                         >  1:796242/1‑147 (MQ=255)                                    gcgcCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATGACCGC‑CGGGGTCCGAcccccgttt                                                                                                           >  2:678901/1‑146 (MQ=255)                                    gcgcCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGGTTATCGGCGGC‑GGGGGGACTTAACGCCACATCACCGC‑TGGCGTCGGACACCGgtt                                                                                                            >  1:937236/1‑150 (MQ=255)                                      gcCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCCCGGTTTATCGGCGGC‑GGGGGGGTTTTAAGCCCCATGACCCC‑CGGGGCCGGGCACCGttttc                                                                                                          >  2:985969/1‑148 (MQ=255)                                                gTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGCTTTAAGCCACATCGCCGC‑CTGCCTCGGGCACCGGTTTGCTGCC‑TTTCa                                                                                               >  1:231782/1‑150 (MQ=255)                                                gTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGGATTTACGCCACCTAAACGC‑CTGCGTCGTGCACCCGTTTGCCGCC‑tttccg                                                                                              >  1:867231/1‑147 (MQ=255)                                                            tctcTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGATTAAAGGCCCAAAACCCCTTGGGGGCGGCAACCGTTTGCCTTCT‑TTCCAGCGACACGGGGa                                                                                   >  1:734952/1‑151 (MQ=255)                                                            tctcTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTAAGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑CTTCCGCGCCACggggga                                                                                  >  1:160299/1‑149 (MQ=255)                                                            tctcTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTTCAGCGACCCGGGGaa                                                                                  >  2:561671/1‑151 (MQ=255)                                                             aacaccggtggtggtGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGGTTTAACGCCACAATACCGC‑CTGCGTCGGGCACCGGTTTGCTTCC‑TTTCCGCGACACGGGGgaa                                                                                 >  1:105341/7‑151 (MQ=255)                                                               ctTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAAAGCCACAAAAACCC‑CGGCGCCCGACACCCGTTTGGTGCCTTTCCGCCGCAACGGGGaaag                                                                                >  1:689894/1‑150 (MQ=255)                                                                        tggtgACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCAt                                                                       <  2:197161/150‑1 (MQ=255)                                                                             aCGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGc                                                                  <  2:199494/150‑1 (MQ=255)                                                                                       ccgcgccgTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTAc                                                        <  1:383514/150‑1 (MQ=255)                                                                                              gTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATTACCCC‑TGGCGGCGGAAACCGTTTTGCCGCC‑TTCCAGCGACCCGGGGAAACGTCCGGCATAACGCAAATCGTTTCCGACCCtt                                                >  2:240196/1‑151 (MQ=255)                                                                                                 aCTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGAt                                             <  1:190817/151‑1 (MQ=255)                                                                                                    ggCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑CTCCAGCGACACGGGGAAACGGCCCGCCTAACGCAAATCGTTACCGACCATTGATAAt                                          >  1:174137/1‑151 (MQ=255)                                                                                                     gCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAAAGCCACATGACCGC‑TGGCGTCGGGCACCGTTTCGCTGCC‑TTTCAGCCACCCCGGGGAAAGTCCCGCCTAACGCAAAACGTTACCCACCATTGATAAtt                                         >  2:436398/1‑151 (MQ=255)                                                                                                     gCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAAt                                          <  1:393168/150‑1 (MQ=255)                                                                                                           aCGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTg                                     <  1:559127/149‑1 (MQ=255)                                                                                                           aCGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTg                                     <  1:575015/149‑1 (MQ=255)                                                                                                            cGGTTAACAAATAGCGGCTCGGTTTTTCGGCGGC‑GGGGAGATTTAAAGCCACATTATCCC‑TGGCGTTGGCCACCGTTTCGCCGCC‑TTCCAGCGACACGGGGGAACGGCCCGCATAACGCAAATCGTTACCCACCCTTTATAATTGCTGAg                                   >  2:992304/1‑150 (MQ=255)                                                                                                              gTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTAACGCCACATGACCGC‑CGGCGTCGGACACCGTTTCGCTGCC‑TTCCCGCGACACGGGGAAACGTCCGGCATAACCCAAATCCTTTCCCACCAtttttcatttttgggcg                                 >  2:919702/1‑135 (MQ=255)                                                                                                                 aaCAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTTACGCCACATGACCGC‑TGGCGTCTGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCa                             >  1:77693/1‑151 (MQ=255)                                                                                                                  aCAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGGTTTAACGCCACATGAACCC‑CGGCGTCGGGCACCGTTTCGCCGGC‑TTTCCTCGGCACGGGGAAACCGCCGGCATAAAGCAAATCGTTACCGACCCTTTATAATTGCTGAgcgcgcca                            >  1:813438/1‑149 (MQ=255)                                                                                                                  aCAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAAAGCAAATCGTTACCCACCATTTATAATTGCTGAGGGGGCaa                            >  2:411356/1‑151 (MQ=255)                                                                                                                  aCAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACAAGACCGC‑TGGCGTCGGACACCGGTTTGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGGTACCGACCATTTATAATTGCTGAGCGCGCaa                            >  2:693926/1‑151 (MQ=255)                                                                                                                    aaaTAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAAc                          <  1:240132/151‑1 (MQ=255)                                                                                                                      aTAGCGGCTCGGTTTATCGGCGGC‑GGGGGGATTTTACCCCACATAACCGC‑TGGCGTCCGCCACCGGTGCGGTGGC‑TTCCCGCGACACGGGGGAACGGCCGGGATAAAGCAAATCGTTACCCACCCCTGATAATTTCCGAgtcgggcaacat                        >  1:122360/1‑140 (MQ=255)                                                                                                                          cGGCTGGGTTTATCGGCGGC‑GGGGAGATTGAACGGCGCATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCAGTGATAATTGCTGAGCGCGCAAACTTAAc                     <  1:836269/150‑1 (MQ=255)                                                                                                                            gCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTg                   <  1:479218/150‑1 (MQ=255)                                                                                                                            gCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTg                   <  2:1007472/150‑1 (MQ=255)                                                                                                                                            gc‑ggGGGGATTTCACGCCACATGACCGC‑TGGCGTCGGGCACCGTTTCGCTGCC‑TTCCAGCCACCCGGGGAAACGTCCGGCATAAAACAAATCGTTACCGAACATTGATAATTGCTGAGCGGGCAAACTTTACTGCACGCCGGCAttttttt  >  1:868696/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                   ATTACTGTATTGTGCGGCAGTACTTAATGAGTAATGCGCCAGACCGCGTTCAATGAGGATCTCTTTGGTGGTGGTGACGCGATACGCCGCGCCGTCACTGGCGGAGACGGTTAACAAATAGCGGCTCGGTTTATCGGCGGC‑GGGGAGATTTAACGCCACATGACCGC‑TGGCGTCGGACACCGTTTCGCTGCC‑TTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTA  >  NC_000913/2332678‑2332967

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑