Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,413,696	T→C	intergenic (‑231/‑168)	envR ← / → acrE	DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,413,696	0	T	C	100.0%	120.9 / NA	32	intergenic (‑231/‑168)	envR/acrE	DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/15);  total (17/15)

GGTTCTTTTTGCCATGATTAATTATTCAGGAAATAAATATATTCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAATATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGATCTCCGCGGCTTTAATCGC  >  NC_000913/3413451‑3413928                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                         ggTTCTTTTTGCCATGATTAATTATTCAGGAAATAAATATATTCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTa                                                                                                                                                                                                                                      <  1:155731/250‑1 (MQ=255)                gATTAATTATTCAGGAAATAAATATATTCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGttt                                                                                                                                                                                                                      >  1:162449/1‑251 (MQ=255)                gATTAATTATTCAGGAAATAAATATATTCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGttt                                                                                                                                                                                                                      >  1:94750/1‑251 (MQ=255)                                         atTCGACACAGAGTGAGAAAATCGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTc                                                                                                                                                                                              >  2:90553/1‑250 (MQ=255)                                           tCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCAt                                                                                                                                                                                            <  2:248307/250‑1 (MQ=255)                                            cGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATa                                                                                                                                                                                           >  2:22286/1‑250 (MQ=255)                                              aaacaGAGGGAGAACATAGAGAAGGCTGATCTATAACCTAATGTGTATTTATACGAGAGGATAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTAAGATGCCTGAATTCATAACt                                                                                                                                                                                        >  2:204017/3‑251 (MQ=255)                                                             aTAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAAGTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATcgac                                                                                                                                                                         <  2:69969/251‑1 (MQ=255)                                                                gCGAAGGTTAATCTATCACCTAATGTGTATTTATACGCGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATcgacga                                                                                                                                                                       >  1:105853/1‑250 (MQ=255)                                                                      gTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATa                                                                                                                                                                 >  1:138598/1‑250 (MQ=255)                                                                                cACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGCCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAAGTTGTAGGa                                                                                                                                                       <  1:74416/250‑1 (MQ=255)                                                                                                ataCGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGGGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTAttttt                                                                                                                                      <  2:147972/251‑1 (MQ=255)                                                                                                  aCGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGGATTtttct                                                                                                                                    <  1:67004/251‑1 (MQ=255)                                                                                                            aaTATTGAGTTGCTATAAATCGGTAAATAAATAATATATAGTATTTACCTAAGATACAGTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTGTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCAGAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACGGGATTTTTCTTTCTGCGAGt                                                                                                                          <  2:133075/251‑1 (MQ=255)                                                                                                                              aTCGTTAAATAAATAATATATATTATTTACCTAAGCTACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTg                                                                                                        >  2:24115/1‑251 (MQ=255)                                                                                                                                    aaataaatAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCGTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTaa                                                                                                   <  2:249097/250‑1 (MQ=255)                                                                                                                                            aataTATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACAGCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTTGGTAAATAAcgcg                                                                                           <  2:163068/250‑1 (MQ=255)                                                                                                                                                   attattTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCAGCGTCAAAATAAAACAGTAGAACATTACTCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAATTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGt                                                                                   >  1:17261/1‑251 (MQ=255)                                                                                                                                                         tACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCTAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACAGCGGCGAAGGATAATTTGTAGGATAGCGAACGGTAATTTTCTTTCTGCGAGTTAATGCTTTGGCTTTTTggtaaagtaactctcattgggtttttt                                                                              <  2:178256/250‑26 (MQ=255)                                                                                                                                                               aGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAAt                                                                       >  1:170531/1‑251 (MQ=255)                                                                                                                                                                     aTTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAAt                                                                 >  2:263737/1‑251 (MQ=255)                                                                                                                                                                     aTTCACTACATCAATATATATTTCAATTTACGAGGTTT‑AATTCTGCCTCTTTCAACCCGCGTCAAAATAACACAGTAGAACATTAATCTTTTTTTGTGTTTATGAGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATg                                                                >  2:263731/1‑251 (MQ=255)                                                                                                                                                                       tCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATg                                                                >  1:34897/1‑250 (MQ=255)                                                                                                                                                                             cATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAAc                                                         <  1:143895/251‑1 (MQ=255)                                                                                                                                                                                  atatatatTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGcc                                                    <  1:301612/251‑1 (MQ=255)                                                                                                                                                                                    atatatTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTGTGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAg                                                  <  1:21900/251‑1 (MQ=255)                                                                                                                                                                                          ttCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCGTTTGGTGTTTTGAGGAATAGTAATGACGAAACATGCCAGGtttt                                             <  1:24115/250‑1 (MQ=255)                                                                                                                                                                                                ttACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGCACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTcctcct                                      >  1:192368/1‑251 (MQ=255)                                                                                                                                                                                                              ttCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTc                        >  1:47329/1‑251 (MQ=255)                                                                                                                                                                                                               tCTGCCTCTTTCAACCCGCGTAAAACTAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCt                       >  2:18280/1‑251 (MQ=255)                                                                                                                                                                                                                  gCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCGTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATTCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGa                     <  2:301475/250‑1 (MQ=255)                                                                                                                                                                                                                                    cAAAATAAAACAGTAGAACATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGATCTCCGCGGCTTTAATCGc  >  2:174431/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                         GGTTCTTTTTGCCATGATTAATTATTCAGGAAATAAATATATTCGACACAGAGTGAGAAAATAGCGAAGGTTAATCTATCACCTAATGTGTATTTATACGAGAGGCTAATATTGAGTTGCTATAAATCGTTAAATAAATAATATATATTATTTACCTAAGATACATTCACTACATCAATATATATTTCAATTTACGAGGTTTTAATTCTGCCTCTTTCAACCCGCGTCAAAATAAAACAGTAGAATATTAATCTTTTTTTGTGTTTATGTGCCTTGAGATGCCTGTATTCATAACTATTCCTTACATCGACGAATGATAATTTGTAGGATAGCGAACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGCCTTTTTGGGTAAATAACGCGCTTTTGGTTTTTTGAGGAATAGTAATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGATCTCCGCGGCTTTAATCGC  >  NC_000913/3413451‑3413928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑