Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,659,977	G→T	R249L (CGC→CTC)	mdtE →	multidrug efflux pump membrane fusion protein MdtE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,659,977	0	G	T	100.0%	125.4 / NA	36	R249L (CGC→CTC)	mdtE	multidrug efflux pump membrane fusion protein MdtE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (21/15);  total (21/15)

ATTTATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACGCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACGGCATTA  >  NC_000913/3659853‑3660107                                                                                                                             |                                                                                                                                   aTTTATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCgg                                                                                                                     >  1:56110/1‑140 (MQ=255) aTTTATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCgg                                                                                                                     >  2:11776/1‑140 (MQ=255)   ttATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCa                                                                                                                   <  1:608647/140‑1 (MQ=255)      tGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGc                                                                                                                >  2:607837/1‑140 (MQ=255)       gTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCt                                                                                                               >  2:585220/1‑140 (MQ=255)           aTCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTCCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGaaa                                                                                                           >  1:605486/1‑140 (MQ=255)                    aGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTccgac                                                                                                  <  1:376349/140‑1 (MQ=255)                     gTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTccgacc                                                                                                 <  1:432009/140‑1 (MQ=255)                        ggTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTccgacccga                                                                                              <  1:240403/140‑1 (MQ=255)                        ggTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTccgacccga                                                                                              <  1:65000/140‑1 (MQ=255)                          tGCAAGATTTCTTACGCATGAAAGAAGAGGACGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACa                                                                                            >  2:164749/1‑140 (MQ=255)                                 tttCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATg                                                                                     <  1:394722/140‑1 (MQ=255)                                    cTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGaaa                                                                                  >  2:581737/1‑140 (MQ=255)                                             gAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCt                                                                         <  2:591268/140‑1 (MQ=255)                                                     agGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACg                                                                 >  1:239012/1‑140 (MQ=255)                                                       gTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGtt                                                               >  2:318413/1‑140 (MQ=255)                                                       gTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGtt                                                               >  1:1611/1‑140 (MQ=255)                                                       gTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGtt                                                               >  1:528154/1‑140 (MQ=255)                                                       gTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGtt                                                               >  1:377566/1‑140 (MQ=255)                                                          gCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACg                                                            >  2:123686/1‑140 (MQ=255)                                                           ccAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACgg                                                           >  1:699552/1‑140 (MQ=255)                                                                       tCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTcccc                                               <  1:164749/140‑1 (MQ=255)                                                                       tCAAACAGGTCCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTcccc                                               <  2:605486/140‑1 (MQ=255)                                                                           aCAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCcccaacc                                           >  2:707034/1‑140 (MQ=255)                                                                                ttCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAAt                                      >  1:279627/1‑140 (MQ=255)                                                                                     ggCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGa                                 >  2:226328/1‑140 (MQ=255)                                                                                             gCCAGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTtgctgc                         <  2:239012/140‑1 (MQ=255)                                                                                                aGTACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTg                      <  1:11776/140‑1 (MQ=255)                                                                                                  tACAGCTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGc                    >  1:754888/1‑140 (MQ=255)                                                                                                       cTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTa               >  2:179466/1‑140 (MQ=255)                                                                                                       cTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTa               >  1:438997/1‑140 (MQ=255)                                                                                                       cTCAATCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTa               >  1:193125/1‑140 (MQ=255)                                                                                                           aTCTGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACTTc           <  1:581737/140‑1 (MQ=255)                                                                                                              tGGAAAATGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACg        <  1:607837/140‑1 (MQ=255)                                                                                                                    aTGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACGGCATTa  <  2:50852/140‑1 (MQ=255)                                                                                                                    aTGGTAAACTCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACGGCATTa  <  1:585220/140‑1 (MQ=255)                                                                                                                             |                                                                                                                                   ATTTATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACGCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACGGCATTA  >  NC_000913/3659853‑3660107

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑