Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	535,925	0	T	G	51.3%	52.2 / 64.3	40	G72G (GGT→GGG)	hyi	hydroxypyruvate isomerase
Reads supporting (aligned to +/- strand):  ref base T (3/16);  new base G (20/0);  total (24/16)
Fisher's exact test for biased strand distribution p-value = 2.57e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.68e-07

CAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAG  >  NC_000913/535785‑536053                                                                                                                                              |                                                                                                                                  cAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTa                                                                                                                         <  1:453523/151‑1 (MQ=255)    tgtgGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGG‑CTGGGGGGCGGGGGGGCGCGGGATTGCCTGttt                                                                                                                        >  1:108656/1‑147 (MQ=255)     gtgGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTGGGGGGCGGGGGGGGGCGGGATTGCCTGTAtt                                                                                                                       >  1:351145/1‑149 (MQ=255)          tttCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGG‑CTGGGGGGCGGGGGGGCGCGGGATTGCCTGTATTCCT‑gggc                                                                                                               >  2:248575/1‑149 (MQ=255)             cgcgGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTGGGGGGCGGGGGGGGGCGGGATTGCCTGTATTTCT‑GGCCggg                                                                                                            >  2:363941/1‑149 (MQ=255)                ggcgTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGGGCGGGATTTGCCGTTTTTCT‑GGcc                                                                                                               >  2:527940/1‑145 (MQ=255)                        aTTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTGTGGGGCGGGGGGGGGCGGGTTTTTCTGTATTCCT‑GGGCGTGGAGAAGAGtt                                                                                                  >  1:240250/1‑150 (MQ=255)                           tATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGG‑CTGGGCGGCGGGGGGGCGCGGGATTGCCTGTATTCCC‑GGCCGGGGAGAAGAGGTTTgg                                                                                              >  1:599133/1‑151 (MQ=255)                                     tATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGG‑ATGGGGGGCGGGGGTGCGCGGGATTCGCTCTATCCCC‑GGGCGTGAAGGAGAAttttcggaggggggtg                                                                                    >  1:497573/1‑138 (MQ=255)                                     tATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑ATGGGGGGCGGGGGGGGGCGGGATTGCCTGTATTTCT‑GGCCGGGGAGAAAAGTTTTggggggggggtg                                                                                    >  2:370663/1‑142 (MQ=255)                                            aCGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTagcagca                                                                               <  1:142105/149‑1 (MQ=255)                                            aCGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGT‑TTGTACTGGGGGGGGGGCCGGCATAATCTGTATTGCT‑GGGCGTGAGAAAGAGTTTCgggggtgcgagg                                                                                    >  1:255513/1‑135 (MQ=255)                                               aCATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTGGGGGGCGGGGGGGGGCGGGATTGCCTGTATTTCT‑GGCCGGGTAGAAGAGGTTCGGGGTGGCGGAGCAGCAGCg                                                                            >  1:644141/1‑149 (MQ=255)                                                    gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGtt                                                                     <  1:337574/151‑1 (MQ=255)                                                    gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGG‑CTGGGGGGCGGGGGGGGGCGGGAATTCCTGTATTTCT‑GGCCGGGGAGAAGAGGTTCGGGGTGGGGGAGCAGCAGCGATTCGtt                                                                     >  1:297821/1‑151 (MQ=255)                                                                   gtgCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTgg                                                      <  2:525673/151‑1 (MQ=255)                                                                    tgCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGG‑CTGGGCGGCGGGGGAGCGCGGGTTTGCCCTTATTCCC‑GGCCGGGGAGAAGGGGTTTGGGGGGGGGGGGCAGGAGGGATTTGGTATGCCCGGGCGCTggg                                                     >  1:63072/1‑151 (MQ=255)                                                                     gCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGCTTCGTTATGCCCGTGCGCTGGGt                                                    <  2:255568/151‑1 (MQ=255)                                                                         gCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGtaata                                                <  2:108683/151‑1 (MQ=255)                                                                         gCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGtaata                                                <  2:599216/151‑1 (MQ=255)                                                                          cGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTTGGCGGCGGGGGGGCGCGGGATTGCCTGTATTTCT‑TGCCGTGAAGAAGAGGTTCGGGGTGGCGGAGCAGCAGCGGTTCGTTTTTCCCGTGCGCTGGGgaata                                                >  2:15560/1‑150 (MQ=255)                                                                                ataaACTCGAACATACGCTGCACAATTTACCGGCGGGGGG‑ATGGGCGGGGGGGGGGCGGGGGATTGCCTTTATTCCT‑GGGCGGGGAGAAGAGGTTTGGGGTGGCGGAGGAGCAGCGATTTGTTATGCCCCTGCGCTGGGGAATaaaaaaa                                          >  1:476082/1‑150 (MQ=255)                                                                                 taaACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGGGGGCGGGATTGCCTGTATTCCT‑GGCCGTGGAGAAGAGTTTCGGGGTGGCGTAGCAGCAGCGATTCGTTATGCCCCGGCGCTGGGGAATaaaaaaaat                                        >  2:469351/1‑149 (MQ=255)                                                                                  aaaCTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAAtt                                        <  2:466212/150‑1 (MQ=255)                                                                                  aaaCTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTa                                       <  1:611086/151‑1 (MQ=255)                                                                                  aaaCTCGAACATACGCTGCACAATTTACCGGCGGGGGAGCTGGG‑GGCGGGGGAGCGGGGGATTGACCGTATTTCTCGTCCGGGAGAATAAGTTTCGGG‑GGGGGTAGCAGGAGCGATTCCGTTTGGACGTGCGCTGGGGTATaaaaaaaat                                        >  1:418526/1‑148 (MQ=255)                                                                                    aCTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑ATGGGCGGCGGGGGGGGGCGGGATTGCCTTTATTTCT‑GGGCGTGAAGAAAAGTTTTGGGGGGGGGTGGCAGAAGCGCATCGTTTTGACCGTGCGCTGGGGAATAAAAAAAATaa                                      >  2:490033/1‑150 (MQ=255)                                                                                      tCGAACATACGCTGCACAATTTACCGGCGGGTGG‑CTGGGGGGCGGGGGGGCGGGGTATTGCCTGTTTTTCT‑TGCCGTGGAGGAGAGGTTCGGGGGGGGGGAGCAGGAGCGATTTGGTATGCCCGGGCGCTGGGGTATAAAAAAATTAAATg                                   >  2:460516/1‑151 (MQ=255)                                                                                       cGAACATACGCTGCACAATTTACCGGCGGGGGA‑CTTGGCGGCGGGGGGGGGCGGGAATTTCTGTTTTCCT‑GGCCGGGGAGAAGAGGTTTGGGGTGGGGTAGCAGCCGCGGTTCGTTTTGGCCGGGCGCTGGGGAATAAAAAAAtt                                        >  2:579650/1‑145 (MQ=255)                                                                                         aaCATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCt                                <  2:326902/151‑1 (MQ=255)                                                                                         aaCATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCt                                <  2:585249/151‑1 (MQ=255)                                                                                          aCATACGCTGCACAATTTACCGGCGGGGGC‑CCGGGCGGTGGGGGAGCCGGGGATTGTCTGGATTGCT‑GGCCGGGCAGAAGAGTTTCGGGGGGGGGTCGAAGCAGCGATTCGTTTTACCCGGGCGCTCGGGAATAAAAAAAATAActctct                                >  2:164483/1‑150 (MQ=255)                                                                                              aCGCTGCACAATTTACCGGCGGGTGA‑CTGGGGGGCGGGGGGGGGCGGGGTTGTCTGTTTTCCT‑TGCCGGGAAGAAGAGTTTCGGGGAGGGGGAGCAGGAGCGATTCGTTTTGGCCGCGGGCTGGGGAATAAAAAAAATAAATGTCttg                              >  2:79036/1‑146 (MQ=255)                                                                                              aCGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCg                           <  2:501368/151‑1 (MQ=255)                                                                                               cGCTGCCCAATTTACCGGCTGGTTA‑CTGTGCGGCGGGGGAGCCCGGTTTTGCCTGTATTCCT‑GGCCGTGAAGTAGAGATTCGGGATGCCGTAGTAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCg                           <  1:695548/150‑1 (MQ=255)                                                                                               cGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTc                            <  1:155454/149‑1 (MQ=255)                                                                                                               ggcggGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGt          <  2:443440/151‑1 (MQ=255)                                                                                                                  gggTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTc       <  1:429352/151‑1 (MQ=255)                                                                                                                      gA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTcagc    >  2:457141/1‑150 (MQ=255)                                                                                                                         cTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTcagcag  >  2:713136/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                  CAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGA‑CTGGGCGGCGGGGGAGCGCGGTATTGCCTGTATTCCT‑GGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAG  >  NC_000913/535785‑536053

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑