Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,356,201	0	T	G	48.8%	40.7 / 13.5	45	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (4/18);  new base G (21/0);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 1.42e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCG  >  NC_000913/1356058‑1356349                                                                                                                                                  |                                                                                                                                                        gTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGG‑GGGGTTaaa                                                                                                                                                   >  1:44108/1‑151 (MQ=255) gTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGTGTTTAAt                                                                                                                                                  >  2:686583/1‑151 (MQ=255)   cATCGGCCCGCGAGGCGCACGGTAACATCGAGGCCGCCGTTTCAGCCGTCCAATAATAGATGGATTGCATCAGGCGCTGGTTATTACTCGCCAGTGCCAGCGCATGGAGGACAGCGTGATTATTTAGCGGAGG‑TTTGGC‑GGTGATAAATGc                                                                                                                                                <  2:624853/151‑1 (MQ=255)       ggCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGGTTAATGCCCGa                                                                                                                                            >  1:816484/1‑151 (MQ=255)             cGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCg                                                                                                                                      <  2:119087/151‑1 (MQ=255)                  cgcgcgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTGGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGtt                                                                                                                                 <  2:673873/151‑1 (MQ=255)                  cgcgcgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGtt                                                                                                                                 <  1:930473/151‑1 (MQ=255)                      cgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTTG‑GGTGGTGAATGCCACGTAGgcggcggtgct                                                                                                                              >  2:118080/1‑145 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑GTTGGG‑GGGGGTAAAAGGCAGATAGGCGGCGTTTATcc                                                                                                                            >  2:543245/1‑150 (MQ=255)                             attgagGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGAc                                                                                                                      <  2:638500/148‑1 (MQ=255)                             atggagGCCGCCGTTTCATCCGTACCATAATAGATGGATTGCATCAGGCGGTTGTTATTAAGCGCCTGTGCCTGCGCAGGGCGGAGAGCGGGATTATTTACCGGCGG‑TTTTGC‑TGTGTTAATGGCCAGATATGCGACGTTCAGCCCAAGAc                                                                                                                      <  2:1067704/148‑1 (MQ=255)                                                   tACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGG‑GGGGTTAATAGCC‑GAGAAGCGAGGGTTATCCCAGGGCCCAGG‑GGTaaaacccagggccg                                                                                               >  2:737064/1‑140 (MQ=255)                                                   tACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGGGTTAAAAGCCACAAAAGGGAAGGTCATCCCCGGACGCCGC‑GGTAAAAGCAAACCCgg                                                                                               >  2:414596/1‑151 (MQ=255)                                                     ccATAATAGATGGATTGCCTCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGCTTATTTAGCGGCGG‑TTTTGC‑TGGGGTAAATGCCAGGTACGGGACCGTCTTCCCCGGAACCCCC‑GTTTAACGCaaaccccggg                                                                                             >  2:804848/1‑143 (MQ=255)                                                     ccATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGG‑GGGGTTAAAT‑CCCGATAGGGGGCGGTCATCCCCGGGCCCCGC‑GTTAAACGCAAACGCgggg                                                                                             >  1:48132/1‑150 (MQ=255)                                                      cATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGCGGTTAATTCCAGATAGGGGAGGTTCATCCCACGACGCAGC‑GGTAAACCCCACCGCGGgtg                                                                                            >  2:725660/1‑150 (MQ=255)                                                         aataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGTTTAATGCCAGATAGGCGGCGGTCATCCCCGGACGCCGC‑GGTAAACGCAAACGCGGggcgt                                                                                          >  1:191921/1‑150 (MQ=255)                                                           taGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGGTTAAAT‑CCCGAGAAGGGGCGTTTCTCTCAGGACCCCAC‑GTTTAAAGCAAgacccgggcggga                                                                                        >  2:988397/1‑138 (MQ=255)                                                             gATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGG‑GGGGTTTAAAGCCAGATAGGGGACGGTTAACCCCGGGCGCAGC‑GGTTAAAGCAAACGCGGggcggtacg                                                                                      >  1:953992/1‑145 (MQ=255)                                                                ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGC‑GGGGTTAAAAGCCCGAAAAGCGACGGTTATCCCCGGACGCCGC‑GTTAAAAGCCAACGCGGGGCGTCACG‑Ccaa                                                                                 >  1:1127364/1‑151 (MQ=255)                                                                ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGGGGTAAAAGCCAGATAGGCGACGTTCATCCCCGGGCGCAGCGGTTAAAGCCAAG‑GCGGGGCGGCCCG‑Caaa                                                                                 >  1:681377/1‑151 (MQ=255)                                                                     gCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGGGTTAAAAGCCAGAAAGGCGGCGTTCATCCCCGGAAGCCGC‑GTTTAAAGCAAGCGCGGGGCGTCACG‑CAAAAAggg                                                                            >  1:1159244/1‑150 (MQ=255)                                                                     gCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGG‑GGGGGTTAAAGCCAAAAAGGGGACGGTCATCCCAGGACGCAGG‑GGTAAAAGCAAACGCGGGGGGGTACG‑CAAAAAGGa                                                                            >  1:864876/1‑151 (MQ=255)                                                                     gCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGTTAAATGCCCGAAAGGCGACGGTTATTCCCGGACGCCGG‑GCTATAAGCCAGCACGGGGCCTCCCG‑CCAAAtagg                                                                            >  2:355924/1‑148 (MQ=255)                                                                        tCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑Ag                                                                        <  2:156884/151‑1 (MQ=255)                                                                           ggCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGG‑GGGGGTTAATGCCACATAAGCGACGCTCATCCCCCGAAGCAGC‑GTTTAACGCAAACGCGGGGCGGCACG‑ACAAAAGGAT‑Ag                                                                        >  2:842499/1‑148 (MQ=255)                                                                            gcgcTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑Agc                                                                       <  2:340539/148‑1 (MQ=255)                                                                               cTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑Agc                                                                       <  1:1020970/145‑1 (MQ=255)                                                                                 ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGG‑GGGGGTAAAAGGCCGAAAAGCGGCGTGTATTCCCGGACGCAGG‑GCTAAAAACCAACGCGGGGCGTCACG‑CAAAAAGGAT‑AActggcggg                                                                >  2:971138/1‑150 (MQ=255)                                                                                 ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGTTTAATGCCAAAAAGGCGACGTTCCTCCCCGGACCCACA‑GGTAAAAGCAAGAGCGGGGGGGCAAG‑CAAAAAGGAA‑AGctggctgg                                                                >  1:419601/1‑150 (MQ=255)                                                                                      ttaATCGCCAGTGCCACCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGGTAAATGCCAGAAAGGGGACGGTCATCCCAGGACGCAGC‑GTTAAAAGGAAGGGCGGGGCGGCACG‑CAAAATGGAA‑AGGTGGGTGGgaggag                                                          >  1:904645/1‑151 (MQ=255)                                                                                         aTCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGcaggcc                                                       <  2:48119/151‑1 (MQ=255)                                                                                            gCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGC‑GGGGGTAAATGCCAAAAAAGCGACGTTCATCCCCCGACGCAGC‑GGTAAAAGCAAGCGCGGGGCGGCCCC‑CCAAAAGGGT‑AACTGGCTGGCAGcagggccgg                                                    >  1:19437/1‑146 (MQ=255)                                                                                                gTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGGGTTAAAAGCCAGAAAGGCGACGGTCATCCCCGGACGCAGC‑GTTAAAAGCAAGGGCGGGGCGGCACC‑CAAAAAGGGA‑AGGTGGGGGGGGGCAGgcccgggcag                                                >  1:1106617/1‑151 (MQ=255)                                                                                                   ccAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAAc                                             <  2:1064794/151‑1 (MQ=255)                                                                                                   ccAGCACATGGCGGACGGCGGGATTATTTGGCGGGGG‑TTTGGC‑GGAGTTAAATGGCAGATAGGCGACGTTCATGACAGTACGGAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAG‑AGCTGGGTGGCAGCGGCGCAGGTCAGAAc                                             <  2:1175192/151‑1 (MQ=255)                                                                                                             gCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTc                                    <  1:88623/150‑1 (MQ=255)                                                                                                             gCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGAAGCAGGCCAGGCCAGAACGTCGCATTc                                    <  2:354817/150‑1 (MQ=255)                                                                                                             gCGGACAGCGGGATTATTTAGCGGCGG‑GTTTGG‑GGTGGTTAATGCCAGATAGGGGGCGGTCATCCCCCGACGCCGC‑GGTTAACGCAAACGCGGGGCGTCACG‑CAAAAAGGGTAAGCTGGC‑GGGGGCAGGCCCGGCCCGAAAGGCGCCttt                                    >  2:70322/1‑149 (MQ=255)                                                                                                              cGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTccc                                  <  1:543511/151‑1 (MQ=255)                                                                                                                         attattTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAg                        <  1:108384/150‑1 (MQ=255)                                                                                                                         attattTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAg                        <  2:407757/150‑1 (MQ=255)                                                                                                                            attTAGCGGCGG‑TTTGGC‑GGTGTTTAATTCCAGATAGGCGACGTTTATTCCACGGCGCCGC‑GCTTAAAGCCAACCCGGGGCGTCACGCCAAAAAGGAA‑GGCT‑GCTGGGCGCCAGCCCGGCCAGGACGGCGCCCTCCCCCGGTAGGAGgttt                    >  2:809970/1‑150 (MQ=255)                                                                                                                                             gC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGTCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTg     <  1:216140/150‑1 (MQ=255)                                                                                                                                              c‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTgc    <  2:334200/150‑1 (MQ=255)                                                                                                                                                 gtgtTAAATGCCAGATAGGCGCCGTTCATCCCCGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCCGGCCAGAACCTCGCATTCCCCGGCCAGGAGGTTCGACCGACGTCCGGTgccg  >  2:571913/1‑150 (MQ=255)                                                                                                                                                 gtgtTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTgccg  >  2:1074727/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                        GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGC‑GGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGC‑GTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAT‑AGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCG  >  NC_000913/1356058‑1356349

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑