Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,534,234	0	G	T	43.2%	51.8 / 17.1	37	E71* (GAG→TAG)	nhoA	N‑hydroxyarylamine O‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base G (1/20);  new base T (16/0);  total (17/20)
Fisher's exact test for biased strand distribution p-value = 1.32e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATTGATACGCTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTTGGTGGAACTGGAAGAGGAAAAAT  >  NC_000913/1534085‑1534378                                                                                                                                                      |                                                                                                                                                   atatTGATACGCTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGa                                                                                                                                                   <  2:531160/151‑1 (MQ=255)      gATACGCTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGa                                                                                                                                              <  1:112576/151‑1 (MQ=255)         aCGCTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATg                                                                                                                                           <  2:988771/151‑1 (MQ=255)            cTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGAAAATGTTTTTAggaaaaa                                                                                                                                            >  2:625136/1‑141 (MQ=255)                   cATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGGTTTTTGCAGAATGGCggggtt                                                                                                                                   >  2:574236/1‑144 (MQ=255)                          ccTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGgtg                                                                                                                         <  1:280748/151‑1 (MQ=255)                              aaaCACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGTGTGTTTG‑AGCGGGTGTTAc                                                                                                                     <  2:1027804/151‑1 (MQ=255)                              aaaCACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACCGTTTTTAGCAGAAAGGCGTGGTTG‑TGCggggggttc                                                                                                                     >  2:290976/1‑145 (MQ=255)                                 cacaATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTAATGTTTTTTGCAGAAAGGGGGGTTTG‑TGgggggggttcg                                                                                                                    >  2:229084/1‑142 (MQ=255)                                   caATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTTCTGTTTTGTGCAGAATCGGGGGGTTG‑GGCGGGGGTTTcgggcg                                                                                                                >  1:249872/1‑147 (MQ=255)                                         cACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTATTGTTTTTTGCAGAATGGCGGGGTTT‑AGGGGGGGGTTCGCGAGG‑Tgggg                                                                                                         >  1:597869/1‑151 (MQ=255)                                                ccGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTTCTGTTTTTAGCAGGAAGGGGGGTTTT‑TGCGGGGGGTACGCGCGC‑TGGGGGTTTACg                                                                                                  >  1:422267/1‑151 (MQ=255)                                                ccGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAAc                                                                                                   <  1:787782/150‑1 (MQ=255)                                                     tGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCg                                                                                              <  2:581713/150‑1 (MQ=255)                                                        aaaCCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGCAGAATGGCGTGGTTG‑TGCGGGGGGTAAGCGGGG‑TGGGGGTTAAAGCTCCCAg                                                                                           >  1:81763/1‑150 (MQ=255)                                                          aCCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCtt                                                                                        <  1:897502/151‑1 (MQ=255)                                                           ccTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGCAGAAAGGGGGGTTTT‑AGCGGGGGGTACGCGAGC‑TGGGGGTTTAAGTTTGCCGCtt                                                                                        >  1:123318/1‑150 (MQ=255)                                                              cGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTa                                                                                    <  2:617162/151‑1 (MQ=255)                                                                 cGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTTGCAGAAAGGGGGGGTTG‑TGCGGGGGGTAGGCGAGCGTGGGGGTTAACG‑TCGCCGCTTGGTAggg                                                                                 >  1:550387/1‑151 (MQ=255)                                                                   ttttGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGGAGAATGGGGTGGTTT‑AGGGGGGGGTTGCCGGGC‑CGGGGTTTTACGTTCGTCGCTTTTTTggggg                                                                               >  2:888612/1‑149 (MQ=255)                                                                     ttGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTGGCAGAATGGGGGGGTTG‑GGGGGGGGGTTCGCGAGC‑TGGGGGTTTAAGTTTGCAGCTTTTTTggggg                                                                               >  1:461639/1‑147 (MQ=255)                                                                      tgctgcCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGcgcg                                                                             <  2:537608/150‑1 (MQ=255)                                                                             gAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTa                                                                     <  2:847672/151‑1 (MQ=255)                                                                                             gATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTTCTTTTTTTAGCAAAATTGCGTGTTTGAAAGGGGGGTTAAGAGACC‑CGGGGGTT‑ATGTTCCCCGCTTGTTACGGCGCGCATGGGTATCAAATCCGc                                                           >  1:782465/1‑145 (MQ=255)                                                                                                    aatcGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTAccgcc                                              <  2:273796/151‑1 (MQ=255)                                                                                                              agagAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCAt                                    <  2:123313/151‑1 (MQ=255)                                                                                                                agaAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATc                                   <  2:955008/150‑1 (MQ=255)                                                                                                                    aCTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGCAGAATGGCGTGTTTT‑AGGGGGGGGTACGCGGGG‑TGGGGGTTAAAGTTCTCCGCTTTTTAGGGCGGGGAGGGGTTTTAAAACCCCCCGCATTTCCCCCCCGCAccccaccctt                               >  1:382419/1‑143 (MQ=255)                                                                                                                     cTGGTGATAGCCCGTCGTGGCGGTTACTTTTTTTTGCAGAATGGGGGGTTTT‑GGCGGGGGGTTAGCGGGC‑TGGGGGGTTAAGTTCCCCGCCTGTTTGGGGGGGGGGGGGTTTCAAAAACCCCCGCATTACCGCCGCGCCCCCCCCGttt                               >  1:321286/1‑149 (MQ=255)                                                                                                                     cTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGCAAAAAGGGGGGTTTT‑AGCGGGGGTTTCGCGGGG‑CGGGGGTTTACGTTCGCAGCCTTTTTGGGCGCGCAGTGTTTTTAAAACCGCCCGCAATTCCCCCCCGCCCCCATCCttt                               >  1:677520/1‑149 (MQ=255)                                                                                                                      tGGTGATAGCCCGTCGTGGCGGTTACTGTTTTTAGCAGAAAGGCGGGTTTT‑TGGGGGGGGTTCGCGCGC‑TGGGGGTTTACGGTCGCCGCTTGTTTGGGCGCGGGGGGGTATTAAATCCCCCCGCCTTTACCCCGCGCCCCCCTCCtt                                >  1:173951/1‑147 (MQ=255)                                                                                                                       ggTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTg                           <  1:315695/151‑1 (MQ=255)                                                                                                                           aTAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTtgg                       <  1:45428/151‑1 (MQ=255)                                                                                                                             aGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTtggtg                     <  1:431753/151‑1 (MQ=255)                                                                                                                               cccGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTTGGTGGa                   <  1:319172/151‑1 (MQ=255)                                                                                                                                         cGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTTGGTGGAACTGGAagag         <  1:879024/151‑1 (MQ=255)                                                                                                                                                 gTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTTGGTGGAACTGGAAGAGGAAAAAt  <  1:304845/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   ATATTGATACGCTTCGTGCATTGCACCTGAAACACAATTGCACCATTCCGTTTGAAAACCTCGACGTTTTGCTGCCGAGGGAAATACAGCTTGATAATCAATCGCCGGAAGAGAAACTGGTGATAGCCCGTCGTGGCGGTTACTGTTTTGAGCAGAATGGCGTGTTTG‑AGCGGGTGTTACGCGAGC‑TGGGGTTTAACGTTCGCAGCTTGTTAGGGCGCGTAGTGTTATCAAATCCGCCAGCATTACCGCCGCGCACCCATCGTTTGCTGTTGGTGGAACTGGAAGAGGAAAAAT  >  NC_000913/1534085‑1534378

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑