Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	395,286	0	G	A	39.0%	53.0 / 12.2	41	F334F (TTC→TTT)	ampH	D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base G (17/8);  new base A (0/16);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 8.99e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGATAACCAACGGTTTATTCCCGCTTAGCTCGGTCACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGATAAATCAACGTC  >  NC_000913/395140‑395436                                                                                                                                                    |                                                                                                                                                        gggATAACCAACGGTTTATTCCCGCTTAGCTCGGTCACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑c                                                                                                                                                    <  1:652695/151‑1 (MQ=255) gggATAACCAACGGTTTATTCCCGCTTAGCTCGGTCACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑c                                                                                                                                                    <  2:309295/151‑1 (MQ=255)              gTTTATTCCCGCTTAGCTCGGTCACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGcc                                                                                                                                       >  1:405066/1‑151 (MQ=255)                ttgttCCCGCTTAGCTCGGCCACCAGGGCATTGATGCCATCGCTCATATTTTTAAAGCGCGTAACCGGCGAACGGGTAACCCCCACAAACCCGCCAATATTCTT‑CTGAGGGTTCATCGCCATATAGGTAATAAAA‑CCGCCACCACCGCCt                                                                                                                                      <  1:147113/147‑1 (MQ=255)                          ttggccggttccccAGGTAATTGATGCCATCGCTCATATTTTAAAAGCGCGCAAGGGGCGAACGAGTGCCCCCCACAAACGCGCAAATATTCTT‑CGGGGGGATCATCCCCATATGGGTAAGAAAA‑CCGCCACCACCGCCTGTCTTCTGa                                                                                                                             <  1:581089/137‑1 (MQ=255)                          ttggCTGGGTCCCCAGGTCTTTGATCCCATCTCTCATATTTTAAAAGCGCGTCAACGGCGAACGAGTAACCCCCAAAAACGCGCCAATTTTTTT‑CGGCGGGATCCTCGCCATAAAGGTAATAAAA‑CCGCCCCCACCGCCTGtcttct                                                                                                                               <  2:249757/144‑1 (MQ=255)                                   ccccaagtatatgattGCCACCGCTAATTTTTTAAAAGCGCGTAAGCGGGGAAGGTGGAACCACCCCAACCGCGCCAATTTTCTT‑CGGGGGGTTCTCCGCAATATAGGTAAGAAAA‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCgg                                                                                                                  <  2:523778/136‑1 (MQ=255)                                    cACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCgg                                                                                                                  >  1:51752/1‑150 (MQ=255)                                          gtaaTTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACCAACGCGCCAATATTCTT‑CTGCGGGTTCATCGCCATCTAGGTAATGCAA‑CCGCCCCCACCGCCTGTCTTCTTCATAATCACCGGACGAccc                                                                                                           >  2:611396/4‑151 (MQ=255)                                           tCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCct                                                                                                          >  1:456090/1‑151 (MQ=255)                                               tGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCttt                                                                                                      >  2:497731/1‑151 (MQ=255)                                                        ccctaatatTTTAAAGGCGGGTCAAGGGGGACCGGGTGCCCCCCACAACCCCCCCAAT‑TTCTTGCTCCGGGAT‑TCCCCCATAATAGTTATGAAACCCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCttt                                                                                                      <  2:473994/137‑1 (MQ=255)                                                        cGCTAATATTTTAAAAGCTGATAAGCGGCGATGGAGAGACCCCCACAAACGCGCAAATATCCTT‑CGGGGGGATCTTCCCCATATAGAAAATAAAC‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGcc                                                                                               <  2:223310/149‑1 (MQ=255)                                                             atatTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCatatat                                                                                         >  1:282523/1‑150 (MQ=255)                                                              tatTTTAAAAGCGCGCAAACGGCAACCGAGTGCCCCCCACAACCGCGCAAATATTCTT‑CGGCGGGATCACCGCCATATGGGTAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCatata                                                                                          <  1:305930/148‑1 (MQ=255)                                                                tttttAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATAccc                                                                                     >  1:133811/1‑151 (MQ=255)                                                                  ttaaaaGCGCGTAACGGGCAAACGGGTGCCCCCCAAAACCGCCCCAATTTTCTT‑CTGCGGGATCATCGCCATATAGGTAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCa                                                                                    <  1:691300/147‑1 (MQ=255)                                                                     aaaGCGCGTCACCGGCAAACGAGTGCCCCCCACAAACGCGCAAATATTCTT‑CTGCGGGATCATCGCCATATAGGAAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAAcc                                                                                 <  1:111114/150‑1 (MQ=255)                                                                     aaaGCGCGTAAAGGGCAAACGAGTGACCCCCAAAACCGCCCCAATATTCTT‑CGGCGGGATCATCGCAATATAGGAAAGGAAC‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAAcc                                                                                 <  2:320055/150‑1 (MQ=255)                                                                      aaGCGCGCCACCGGGGACCGAGTGACCCCCACAACCGCCCAAATATTCTT‑CTGCGGGTTCATCGCCATATAGGAAATGAAC‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTa                                                                               <  2:48882/151‑1 (MQ=255)                                                                              cAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAgc                                                                       >  1:313277/1‑151 (MQ=255)                                                                                  ggggAAGGAGGGACCACCACAAACGCGCAAATATTCTT‑CTGCGGGATCACCGCCATATAGATAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCAt                                                                   <  1:294951/148‑1 (MQ=255)                                                                                    cGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATcc                                                                 >  2:30819/1‑151 (MQ=255)                                                                                      aaCGAGTGCCCCCCACAAACGCGCAAATATTCTT‑CTGCGGGACCATCCCCATATAGTTAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATc                                                                  <  2:327668/148‑1 (MQ=255)                                                                                       aCGAGTGACCCCCAAAACCGCCCGAATATTCTT‑CGGCGGATTCACCCCAATAT‑GGTAAAAAAACCCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCt                                                              <  2:127002/151‑1 (MQ=255)                                                                                         gggTGACCCCCACAACCCCGCCAATATTCTT‑CTGCGGGATCATCGCCATATA‑GTAAAGAAACCCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCttt                                                            <  2:109135/149‑1 (MQ=255)                                                                                         gAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCttt                                                            >  2:519506/1‑151 (MQ=255)                                                                                            ggccccccccaAACCCGCCATTATTCTT‑CTGGGTGTGAACCCCAATATGGGAAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGcc                                                         <  2:467321/142‑1 (MQ=255)                                                                                               ccaccaCAAACCGCCCAATTTTCTC‑CTGGGGGTTCTTCGCAAAAGAGTTAATAAAA‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCggg                                                      <  2:533170/151‑1 (MQ=255)                                                                                                      aacccccccAATATTTTT‑CTGCGGTATCATCGCAATAAAGTTAATAAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACa                                                  <  1:100186/141‑1 (MQ=255)                                                                                                                          tGCGGGATCATCGCCATATAGGTAATGACA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATAACTTTCg                               >  2:520233/1‑148 (MQ=255)                                                                                                                           gCGGGTTCACCCCCAAATAGTAAAAGAAA‑CCGCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTaa                            <  2:51744/150‑1 (MQ=255)                                                                                                                             gggaccaccccaataaAGGTAAAAAAC‑CCCCCCCCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTaa                            <  2:348268/136‑1 (MQ=255)                                                                                                                              ggATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTg                        >  2:322922/1‑151 (MQ=255)                                                                                                                                atcatcGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTgcg                      >  1:614629/1‑151 (MQ=255)                                                                                                                                     cGCCATATGGGTAATAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTgcgcgcg                  <  1:303245/150‑1 (MQ=255)                                                                                                                                          tataGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGAt             >  1:477695/1‑150 (MQ=255)                                                                                                                                          tataGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGAt             >  2:536333/1‑150 (MQ=255)                                                                                                                                            taGGAAATGAAA‑GAGGTACTACCGACTGTTTTCTGAATAATCTACGGACGATCCTATTTCGGGGCCATATATACCAAACGTAAACCAAGCGCATCCGCTTTGACGGGGACATCCATGCAAATCACTTTAGTAAACTGCGCGTGCTGATa            >  2:149516/1‑149 (MQ=255)                                                                                                                                               gTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGATAAATc        >  1:120596/1‑150 (MQ=255)                                                                                                                                                 aaTAAAC‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGATAAATCaa      <  1:193395/150‑1 (MQ=255)                                                                                                                                                    gAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGATAAATCAACGTc  >  2:471932/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                        GGGATAACCAACGGTTTATTCCCGCTTAGCTCGGTCACCAGGTCATTGATGCCATCGCTCATATTTTTAAAGCGCGTCAACGGCGAACGAGTGACCACCACAAACGCGCCAATATTCTT‑CTGCGGGATCATCGCCATATAGGTAATGAAA‑CCGCCACCACCGCCTGTCTTCTGAATAATCCCCGGACGACCCTCTTTCGGGGCCATATATACCCAACCTAAACCAAGCGCATCCGCTTTGCCGGGGACATCCATGCCAATCACTTTCGTAAACTGCGCGCGCTGATAAATCAACGTC  >  NC_000913/395140‑395436

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑