Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,891,677	G→A	M21I (ATG→ATA)	mdtL →	efflux pump MdtL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,891,677	0	G	A	100.0%	113.5 / NA	34	M21I (ATG→ATA)	mdtL	efflux pump MdtL
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/18);  total (16/18)

TGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCC  >  NC_000913/3891437‑3891906                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                       tgtgCGGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCTCTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATCCCTCGtt                                                                                                                                                                                                                               <  2:36570/250‑1 (MQ=255)       ggTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTa                                                                                                                                                                                                                         <  1:207875/250‑1 (MQ=255)                aCGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATcg                                                                                                                                                                                                               >  2:244040/1‑251 (MQ=255)                      ttAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGTACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTTGTTTTACTTTACCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCgccgcc                                                                                                                                                                                                          <  1:386966/250‑1 (MQ=255)                       tAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGccgccg                                                                                                                                                                                                         >  1:105288/1‑250 (MQ=255)                         aCGTGTTACCTAAATTTGACTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTGCTTGCCTCTCAGGAAATCACTTATGTCCAAAGGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCCCCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTCCTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGAtc                                                                                                                                                                                                      <  1:359051/251‑1 (MQ=255)                                    aaaTTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGTTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATCCCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑g                                                                                                                                                                                           <  1:257305/250‑1 (MQ=255)                                         tGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAg                                                                                                                                                                                      <  1:226204/250‑1 (MQ=255)                                              aaaTCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCACCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATTCCA‑GCGAAGCGCAg                                                                                                                                                                                 <  1:275087/250‑1 (MQ=255)                                               aaTCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGACCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGCTCTCAATGCCA‑GCGAAGCGCAGtt                                                                                                                                                                               >  1:7084/1‑251 (MQ=255)                                                aTCCTTCAAGAAGCCAGCCCTTCGCTGGCTTCTTGCCTCTCAGGCAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCCTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTCTCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCCGTTg                                                                                                                                                                              >  1:41625/1‑251 (MQ=255)                                                                 tcaTTCGATGGGTTCATGCCTCTCAGGAAATCACTTATGACCATATGCCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTACCTTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGCTTACCGCGCATCCCCGCCGATCTCAAT‑CCACGCGACGCGCAGTTCCATATTACGTTCTCCGt                                                                                                                                                             >  2:403766/2‑251 (MQ=255)                                                                 ccaTTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGt                                                                                                                                                             <  1:71126/251‑1 (MQ=255)                                                                                    ctctCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGc                                                                                                                                           >  2:106956/1‑250 (MQ=255)                                                                                                 aCTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTAt                                                                                                                             >  2:308649/1‑251 (MQ=255)                                                                                                    tATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGTAGCTGCGATGTTAtt                                                                                                                            <  1:147251/249‑1 (MQ=255)                                                                                                               ggCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTg                                                                                                               <  1:224724/251‑1 (MQ=255)                                                                                                                      cGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATc                                                                                                        <  1:249914/251‑1 (MQ=255)                                                                                                                       gggtGATCATCCTGCACCACGTACTCTTTGCGCCAGCTTAATATAATCACGCTTTAGCCCATGTCCAGATTTTTAATTTGTAGTTTTGCCATGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCTTTGTTTTCTAGCGCATCGCCGCCGATCTCAATGCCA‑GAGAAGCGCAGTTGCATATAGCGTTCTCAGTATATACGGCGGCGATGGCAGCAGCGATGTTATCTGCCGGTAAAgataccgacct                                                                                                       >  2:90882/4‑241 (MQ=255)                                                                                                                             tcctccTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAgg                                                                                                 >  2:146122/1‑251 (MQ=255)                                                                                                                                         acGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCCGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCCGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGt                                                                                     >  2:200562/1‑251 (MQ=255)                                                                                                                                                       tCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGAAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCAGGTCGCCATACAcggcg                                                                       >  1:103666/1‑251 (MQ=255)                                                                                                                                                                 aTCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCtatt                                                             >  2:324013/1‑251 (MQ=255)                                                                                                                                                                                  cATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGACTCGgtgt                                            >  1:416287/1‑251 (MQ=255)                                                                                                                                                                                     gTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGtgttct                                         <  1:197150/251‑1 (MQ=255)                                                                                                                                                                                      tCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTACCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGtgttct                                         <  1:63529/250‑1 (MQ=255)                                                                                                                                                                                               ttGATTTGTAGTTTTGCCCTGGTTTTAATTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGGGTTCTGTTCACTGGc                               >  2:265991/1‑251 (MQ=255)                                                                                                                                                                                                  aTTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGa                            <  1:296529/251‑1 (MQ=255)                                                                                                                                                                                                                   ggTTTTACTTTATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTAttt            <  1:244040/250‑1 (MQ=255)                                                                                                                                                                                                                   ggTTTTACTTTATACCGCCGGGATTGATATATACCACGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGACA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGACGTTATTTGCCGGTAAAGGGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGGGCGGCGCGATTTATTATTGCCTCGGTGTTCTGTTCACTGGCGGAAACAGGCACGGTATTTc           >  2:191708/1‑251 (MQ=255)                                                                                                                                                                                                                    gttttacgtgagcccGCCGGGATTGATATATACCTCGTGGGTTTACGGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCATGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATGGCCTCGGTGTTCTGTGCACTGGCTGAAACCAGCACGTTATTTCt          <  2:276453/239‑1 (MQ=255)                                                                                                                                                                                                                     ttttACTTTATCCCGCCGGGATTGATATATACCTCGCTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGCAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGAAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAACCCGGTCGCCATACCCGGCGCGGCGCTCTTTCTTATTGCTTCGGCGTTCCGTTCACTGGCGGAAACCAGCAAGTTATTTCtt         >  2:40206/1‑251 (MQ=255)                                                                                                                                                                                                                         actgtATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCa      <  1:142620/246‑1 (MQ=255)                                                                                                                                                                                                                             tATCCCGCCGGGATTGATATATACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGcc  <  1:146122/250‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                       TGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCA‑GCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCC  >  NC_000913/3891437‑3891906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑