Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,892,455	G→A	A281T (GCG→ACG)	mdtL →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,892,455	0	G	A	100.0%	178.0 / NA	56	A281T (GCG→ACG)	mdtL	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/29);  total (27/29)

ACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGC  >  NC_000913/3892338‑3892589                                                                                                                      |                                                                                                                                       accgTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGttt                                                                                                                   >  1:914070/1‑139 (MQ=255)   caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                 <  2:225746/123‑1 (MQ=255)   caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                 >  1:225746/1‑123 (MQ=255)   caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCa                                                                                                                 >  1:928976/1‑139 (MQ=255)        tGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTc                                                                                                            >  1:869867/1‑139 (MQ=255)        tGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTc                                                                                                            <  2:869867/139‑1 (MQ=255)           cgcTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCa                                                                                                         <  2:403205/139‑1 (MQ=255)             cTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                       >  1:799250/1‑139 (MQ=255)              tGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCg                                                                                                                      <  2:6172/123‑1 (MQ=255)              tGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCg                                                                                                                      >  1:6172/1‑123 (MQ=255)                aCCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCgg                                                                                                    >  1:46155/1‑139 (MQ=255)                     tGGCGTCATCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                               <  1:1252271/139‑1 (MQ=255)                     tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                               <  2:914070/139‑1 (MQ=255)                     tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                               <  1:774892/139‑1 (MQ=255)                          tCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCg                                                                                                     <  2:942666/128‑1 (MQ=255)                          tCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCg                                                                                                     >  1:942666/1‑128 (MQ=255)                               aTGACCGTTTCGTTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCAGCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                     <  1:871669/139‑1 (MQ=255)                                  aCCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCAc                                                                                                                              >  2:684725/1‑95 (MQ=255)                                  aCCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCAc                                                                                                                              <  1:684725/95‑1 (MQ=255)                                  aCCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCa                                                                                  >  1:826370/1‑139 (MQ=255)                                        tCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGa                                                                            >  2:38603/1‑139 (MQ=255)                                                cACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGcc                                                                    <  2:46155/139‑1 (MQ=255)                                                     cATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGttt                                                               >  2:445585/1‑139 (MQ=255)                                                     cATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGttt                                                               <  1:541094/139‑1 (MQ=255)                                                        ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                 <  2:1311400/70‑1 (MQ=255)                                                        ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                 >  1:1311400/1‑70 (MQ=255)                                                         tGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCg                                                           <  2:177560/139‑1 (MQ=255)                                                           cgcTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                         <  1:746217/139‑1 (MQ=255)                                                                      tttAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCCTGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGgtg                                              <  2:1328377/139‑1 (MQ=255)                                                                            ccACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGa                                        <  1:38603/139‑1 (MQ=255)                                                                              acgtacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGa                                        <  2:22725/137‑1 (MQ=255)                                                                              acgtacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGa                                        >  1:22725/1‑137 (MQ=255)                                                                                gtacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGttt                                                   <  1:100096/124‑1 (MQ=255)                                                                                gtacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGttt                                                   >  2:100096/1‑124 (MQ=255)                                                                                 tacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGt                                   <  2:826370/139‑1 (MQ=255)                                                                                  acgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTc                                  <  1:691691/139‑1 (MQ=255)                                                                                      tgatgaTCACCTCGCAGGTGTTATTCCTGgcgacg                                                                                                                                      >  2:529471/1‑35 (MQ=255)                                                                                           atCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAg                         >  1:1207707/1‑139 (MQ=255)                                                                                            tCACCTCGTAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGttt                                                                                                 <  2:957228/66‑1 (MQ=255)                                                                                            tCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGttt                                                                                                 >  1:957228/1‑66 (MQ=255)                                                                                             cACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAggg                       >  2:1107799/1‑139 (MQ=255)                                                                                              aCCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                               <  2:347896/66‑1 (MQ=255)                                                                                              aCCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                               >  1:347896/1‑66 (MQ=255)                                                                                               ccTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCCCCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGcc                     >  2:650095/1‑139 (MQ=255)                                                                                                  cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                     <  1:199517/72‑1 (MQ=255)                                                                                                  cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                     >  2:199517/1‑72 (MQ=255)                                                                                                  cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGtt                  >  1:734383/1‑139 (MQ=255)                                                                                                    cAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTgcgc                                                                     >  2:455882/1‑86 (MQ=255)                                                                                                    cAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTgcgc                                                                     <  1:455882/86‑1 (MQ=255)                                                                                                    cAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGtttt                >  2:828416/1‑139 (MQ=255)                                                                                                        tgtTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCAtt            <  2:928976/139‑1 (MQ=255)                                                                                                          ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCg                    >  2:597679/1‑129 (MQ=255)                                                                                                          ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCg                    <  1:597679/129‑1 (MQ=255)                                                                                                          ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTAc          >  2:573293/1‑139 (MQ=255)                                                                                                             ttCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTAcgcg       <  1:721191/139‑1 (MQ=255)                                                                                                             ttCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTAcgcg       <  1:1107799/139‑1 (MQ=255)                                                                                                                 tGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCggg   >  1:503836/1‑139 (MQ=255)                                                                                                                  ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                       >  2:1064700/1‑38 (MQ=37)                                                                                                                  ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                       <  1:1064700/38‑1 (MQ=37)                                                                                                                  ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGc  >  2:565326/1‑139 (MQ=255)                                                                                                                  ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGc  >  1:681976/1‑139 (MQ=255)                                                                                                                  ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGc  >  1:748412/1‑139 (MQ=255)                                                                                                                      |                                                                                                                                       ACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGC  >  NC_000913/3892338‑3892589

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑