Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,853,966	A→G	L15L (TTA→TTG)	emrD →	multidrug efflux pump EmrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,853,966	0	A	G	100.0%	193.2 / NA	54	L15L (TTA→TTG)	emrD	multidrug efflux pump EmrD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/27);  total (27/27)

ATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGTG  >  NC_000913/3853839‑3854093                                                                                                                                |                                                                                                                                atcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTc                                                                                                                     >  2:370176/1‑140 (MQ=255) atcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTc                                                                                                                     >  1:648309/1‑140 (MQ=255)        tgATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGa                                                                                                              >  2:253496/1‑140 (MQ=255)             gATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGgcg                                                                                                         <  1:448200/140‑1 (MQ=255)              aTTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGC‑AAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCa                                                                                                       <  1:129461/140‑1 (MQ=255)                tCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCaa                                                                                                      <  2:366823/140‑1 (MQ=255)                tCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCaa                                                                                                      <  1:830230/140‑1 (MQ=255)                tCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCaa                                                                                                      >  1:646629/1‑140 (MQ=255)                  ctctCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGa                                                                                                              >  1:812631/1‑130 (MQ=255)                  ctctCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGa                                                                                                              <  2:812631/130‑1 (MQ=255)                   tctcCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAAcc                                                                                                   <  1:370176/140‑1 (MQ=255)                    ctcCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCa                                                                                                       >  1:388596/1‑135 (MQ=255)                    ctcCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCa                                                                                                       <  2:388596/135‑1 (MQ=255)                     tcCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCAt                                                                                                 >  2:580641/1‑140 (MQ=255)                     tcCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCAt                                                                                                 >  2:685325/1‑140 (MQ=255)                        cGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTta                                                                                              <  1:214116/140‑1 (MQ=255)                              tATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTcc                                                                                        <  2:823817/140‑1 (MQ=255)                               aTGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCa                                                                                       >  1:800551/1‑140 (MQ=255)                               aTGGGAATGCGTAGTGACTTATTCTAATTATTTTCATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTta                                                                                              <  2:770105/133‑1 (MQ=255)                               aTGGGAATGCGTAGTGACTTATTCTAATTATTTTCATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTta                                                                                              >  1:770105/1‑133 (MQ=255)                                 gggAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGc                                                                                     >  1:726259/1‑140 (MQ=255)                                      tGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTg                                                                                >  1:539510/1‑140 (MQ=255)                                       gCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGc                                                                               >  2:583122/1‑140 (MQ=255)                                          tAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGa                                                                            >  2:699758/1‑140 (MQ=255)                                                   aTTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGgcgcg                                                                   <  1:583122/140‑1 (MQ=255)                                                   aTTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGgcgcg                                                                   <  2:646629/140‑1 (MQ=255)                                                    ttCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGgcgcgc                                                                  >  1:496493/1‑140 (MQ=255)                                                     tCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGcgcgcg                                                                 <  2:911178/140‑1 (MQ=255)                                                     tCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGcgcgcg                                                                 <  2:574570/140‑1 (MQ=255)                                                     tCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGcgcgcg                                                                 <  1:827384/140‑1 (MQ=255)                                                     tCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGCATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGcgcgcg                                                                 >  1:374032/1‑140 (MQ=255)                                                         attattTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGAtct                                                             >  1:880643/1‑140 (MQ=255)                                                                     aaaGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGa                                                 <  1:175763/140‑1 (MQ=255)                                                                       aGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAg                                               <  2:880643/140‑1 (MQ=255)                                                                       aGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAg                                               >  2:829409/1‑140 (MQ=255)                                                                         cATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAggg                                             <  2:272433/140‑1 (MQ=255)                                                                           tCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGc                                           >  1:739201/1‑140 (MQ=255)                                                                           tCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGc                                           >  2:686498/1‑140 (MQ=255)                                                                             cGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCgg                                         >  2:214678/1‑140 (MQ=255)                                                                               tGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTCAAGGGGCGGTg                                       <  2:648309/140‑1 (MQ=255)                                                                                gATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGc                                      <  2:739201/140‑1 (MQ=255)                                                                                gATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGc                                      <  2:496493/140‑1 (MQ=255)                                                                                 aTAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCa                                     <  1:484937/140‑1 (MQ=255)                                                                                       aaaaGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGt                               >  1:502257/1‑140 (MQ=255)                                                                                          aGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAAt                            >  2:745946/1‑140 (MQ=255)                                                                                             cAAAGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATggg                         <  1:619392/140‑1 (MQ=255)                                                                                               aaGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTa                              >  2:129179/1‑133 (MQ=255)                                                                                               aaGAAACGTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTa                              <  1:129179/133‑1 (MQ=255)                                                                                                      gTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCtt                    >  2:742911/1‑136 (MQ=255)                                                                                                      gTCAATTTGTTATTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCtt                    <  1:742911/136‑1 (MQ=255)                                                                                                         aaTTTGTTATTGATGTTGGTATTGCTGGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATctgct             <  2:527205/140‑1 (MQ=255)                                                                                                                 tattaTGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACg     >  1:572615/5‑140 (MQ=255)                                                                                                                 aTTGATGTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACg     <  1:253496/140‑1 (MQ=255)                                                                                                                       gTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGgtg  <  2:190011/137‑1 (MQ=255)                                                                                                                       gTTGGTATTGCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGgtg  >  1:190011/1‑137 (MQ=255)                                                                                                                                |                                                                                                                                ATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGTG  >  NC_000913/3853839‑3854093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑