Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,162,744	C→A	T427T (ACC→ACA)	mdtD →	putative multidrug efflux pump MdtD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,162,744	0	C	A	100.0%	197.4 / NA	56	T427T (ACC→ACA)	mdtD	putative multidrug efflux pump MdtD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (34/22);  total (34/22)

CGGACAATCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACCACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAGCGCGCAATG  >  NC_000913/2162611‑2162878                                                                                                                                      |                                                                                                                                       cGGACAATCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGcacaacacaa                                                                                                                                  >  1:442064/1‑140 (MQ=255)  ggACAATCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACaaa                                                                                                                                 <  2:1428959/140‑1 (MQ=255)        tCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCATAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCt                                                                                                                           <  2:1513089/140‑1 (MQ=255)        tCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCt                                                                                                                           >  1:999721/1‑140 (MQ=255)        tCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCt                                                                                                                           <  2:500056/140‑1 (MQ=255)        tCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCt                                                                                                                           >  2:1496639/1‑140 (MQ=255)          tGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCttt                                                                                                                         >  1:791201/1‑140 (MQ=255)                 cagcGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTaca                                                                                                                  <  2:92548/140‑1 (MQ=255)                  agcGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTacac                                                                                                                 >  2:1362019/1‑140 (MQ=255)                   gcGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACAcc                                                                                                                <  2:110504/140‑1 (MQ=255)                          cAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTg                                                                                                              >  1:447455/1‑135 (MQ=255)                          cAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTg                                                                                                              <  2:447455/135‑1 (MQ=255)                                       atgatTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGat                                                                                            >  1:324928/1‑140 (MQ=255)                                          atTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGatcat                                                                                         <  2:791201/140‑1 (MQ=255)                                           ttATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGatcatc                                                                                        >  1:1332910/1‑140 (MQ=255)                                              tGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGatccgccct                                                                                     >  2:667606/1‑134 (MQ=255)                                              tGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGcc                                                                                     >  1:1235139/1‑140 (MQ=255)                                                  aTTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTc                                                                                 <  2:863442/140‑1 (MQ=255)                                                    tGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCg                                                                               >  1:1125265/1‑140 (MQ=255)                                                     gTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCgg                                                                              >  1:102691/1‑140 (MQ=255)                                                      tCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTc                                                                                 <  1:1236909/136‑1 (MQ=255)                                                      tCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTc                                                                                 >  2:1236909/1‑136 (MQ=255)                                                      tCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGc                                                                             >  1:1378525/1‑140 (MQ=255)                                                        gATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGt                                                                           <  1:914642/140‑1 (MQ=255)                                                        gATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGt                                                                           <  2:1378525/140‑1 (MQ=255)                                                                tCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCttt                                                                   >  1:1321286/1‑140 (MQ=255)                                                                  ggCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATC‑‑CGCCCTTCCGGCGTTCATCTTTGCCa                                                               <  1:667606/140‑1 (MQ=255)                                                                   gCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGcc                                                                >  2:1326958/1‑140 (MQ=255)                                                                    cGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCa                                                               <  2:999721/140‑1 (MQ=255)                                                                      tCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGTATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCa                                                               >  1:285585/1‑138 (MQ=255)                                                                      tCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGTATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCa                                                               <  2:285585/138‑1 (MQ=255)                                                                      tCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCaga                                                             >  2:159084/1‑140 (MQ=255)                                                                         cTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTg                                                          <  1:1496639/140‑1 (MQ=255)                                                                         cTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTg                                                          <  2:442064/140‑1 (MQ=255)                                                                          tATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGc                                                         >  1:1221637/1‑140 (MQ=255)                                                                              gCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGaa                                                     >  1:1018535/1‑140 (MQ=255)                                                                                  ggCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGAt                                                 >  2:959420/1‑140 (MQ=255)                                                                                   gCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATa                                                >  1:1219673/1‑140 (MQ=255)                                                                                   gCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATa                                                >  1:1443186/1‑140 (MQ=255)                                                                                         gCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATc                                          <  1:1362019/140‑1 (MQ=255)                                                                                            gggACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCaaa                                       >  2:760571/1‑140 (MQ=255)                                                                                            gggACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCaaa                                       >  1:858329/1‑140 (MQ=255)                                                                                            gggACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCaaa                                       >  1:1524884/1‑140 (MQ=255)                                                                                                 tttttGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCaaaa                                      <  1:195133/136‑1 (MQ=255)                                                                                                 tttttGGTTCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCaaaa                                      >  2:195133/1‑136 (MQ=255)                                                                                                         tCACAGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTc                          >  1:914649/1‑140 (MQ=255)                                                                                                           acaGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTcgc                        <  1:959420/140‑1 (MQ=255)                                                                                                             aGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCgcgg                      >  2:1315249/1‑140 (MQ=255)                                                                                                             aGCATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCgcgg                      >  1:1072842/1‑140 (MQ=255)                                                                                                               cATGTCAGCGTCGACAGCGGCACAACACAAACCGTCTTTATGAACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCgcggcg                    >  2:337595/1‑140 (MQ=255)                                                                                                                       cGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGa            <  2:1443186/140‑1 (MQ=255)                                                                                                                       cGTCGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGa            >  1:601033/1‑140 (MQ=255)                                                                                                                          cGACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAgcg         <  2:1221637/140‑1 (MQ=255)                                                                                                                           gACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAgcgc        >  1:1479906/1‑140 (MQ=255)                                                                                                                           gACAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAgcgc        >  1:1176149/1‑140 (MQ=255)                                                                                                                            aCAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAgcgcg       <  2:1235139/140‑1 (MQ=255)                                                                                                                            aCAGCGGCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAgcgcg       >  2:814386/1‑140 (MQ=255)                                                                                                                                 ggCACAACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAGGGCGCAATg  <  2:310781/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       CGGACAATCTGGCGAGCAGCGGCAACAGCCTGCTGTCGATGATTATGCAATTGTCGATGAGTATCGGCGTCACTATCGCCGGGCTGTTGCTGGGACTTTTTGGTTCACAGCATGTCAGCGTCGACAGCGGCACCACACAAACCGTCTTTATGTACACCTGGCTTAGCATGGCGTTGATCATCGCCCTTCCGGCGTTCATCTTTGCCAGAGTGCCGAACGATACGCATCAAAATGTAGCTATTTCGCGGCGAAAAAGGAGCGCGCAATG  >  NC_000913/2162611‑2162878

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: ‑