Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,286,821	C→T	A21A (GCC→GCT)	lpoA →	penicillin‑binding protein activator LpoA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,286,821	0	C	T	100.0%	249.9 / NA	63	A21A (GCC→GCT)	lpoA	penicillin‑binding protein activator LpoA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/34);  total (29/34)

TGTCGTCCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCCCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCTGATGATACCAGGATCAACTGGC  >  NZ_CP009273/3286697‑3286954                                                                                                                              |                                                                                                                                      tgtCGTCCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCgg                                                                                                                         <  2:323567/139‑1 (MQ=255)   tcgtcCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGtt                                                                                                                       >  2:411393/1‑139 (MQ=255)   tcgtcCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGtt                                                                                                                       >  2:443406/1‑139 (MQ=255)     gtcCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTtgt                                                                                                                     <  2:107305/139‑1 (MQ=255)      tcCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTtgtg                                                                                                                    >  2:571291/1‑139 (MQ=255)      tcCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTtgtg                                                                                                                    >  2:637828/1‑139 (MQ=255)          tATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCAc                                                                                                                >  1:793810/1‑139 (MQ=255)              gCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  1:411856/138‑1 (MQ=255)              gCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  1:646113/138‑1 (MQ=255)              gCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  1:606196/138‑1 (MQ=255)                  aTTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTc                                                                                                        <  1:379050/139‑1 (MQ=255)                             aGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTgg                                                                                                                   >  2:66905/1‑117 (MQ=255)                             aGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTgg                                                                                                                   <  1:66905/117‑1 (MQ=255)                             aGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  2:225423/123‑1 (MQ=255)                             aGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             >  1:225423/1‑123 (MQ=255)                             aGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTc                                                                                              >  2:598892/1‑138 (MQ=255)                               cATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  1:587244/139‑1 (MQ=255)                                    cGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGc                                                                                                                  >  1:758583/1‑111 (MQ=255)                                    cGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGc                                                                                                                  <  2:758583/111‑1 (MQ=255)                                    cGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  2:669226/134‑1 (MQ=255)                                    cGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           >  1:669226/1‑134 (MQ=255)                                       aaaaaaaaTATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTtata                                                                                   >  2:238566/1‑139 (MQ=255)                                           aaaaTATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCa                                                                               <  1:571291/139‑1 (MQ=255)                                                              tATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGAt                                                                                                   <  1:629620/100‑1 (MQ=255)                                                              tATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGAt                                                                                                   >  2:629620/1‑100 (MQ=255)                                                                 ggTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCt                                                         >  2:304470/1‑139 (MQ=255)                                                                  gTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCt                                                         <  1:424679/138‑1 (MQ=255)                                                                  gTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTg                                                        >  2:579339/1‑139 (MQ=255)                                                                   tACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  2:92017/85‑1 (MQ=255)                                                                   tACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             >  1:92017/1‑85 (MQ=255)                                                                   tACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAgg                                                                 <  2:557098/129‑1 (MQ=255)                                                                   tACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAgg                                                                 >  1:557098/1‑129 (MQ=255)                                                                      ccTCAACATTTTCTCGGTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  1:539087/83‑1 (MQ=255)                                                                      ccTCAACATTTTCTCGGTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             >  2:539087/1‑83 (MQ=255)                                                                      ccTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGgcg                                                                     <  2:551085/122‑1 (MQ=255)                                                                      ccTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGgcg                                                                     >  1:551085/1‑122 (MQ=255)                                                                      ccTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCtt                                                    >  2:695117/1‑139 (MQ=255)                                                                      ccTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCtt                                                    <  2:118260/139‑1 (MQ=255)                                                                        tCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             >  1:171315/1‑80 (MQ=255)                                                                        tCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCa                                                                                                             <  2:171315/80‑1 (MQ=255)                                                                        tCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCttt                                                   >  1:654217/1‑138 (MQ=255)                                                                          aaCATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGAt                                                                                                   >  1:392266/1‑88 (MQ=255)                                                                          aaCATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGAt                                                                                                   <  2:392266/88‑1 (MQ=255)                                                                          aaCATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           >  2:582924/1‑96 (MQ=255)                                                                          aaCATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  1:582924/96‑1 (MQ=255)                                                                          aaCATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTAt                                                >  2:516813/1‑139 (MQ=255)                                                                                            aaGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATgcagca                               <  1:238566/139‑1 (MQ=255)                                                                                                 gcgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGct                          <  1:325803/139‑1 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           >  1:109558/1‑73 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           >  2:354168/1‑73 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  1:664401/73‑1 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  2:109558/73‑1 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           <  1:354168/73‑1 (MQ=255)                                                                                                  cgcgTTGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCAc                                                                                           >  2:664401/1‑73 (MQ=255)                                                                                                      ttGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCtgat                     <  1:355213/139‑1 (MQ=255)                                                                                                      ttGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCtgat                     <  2:793810/139‑1 (MQ=255)                                                                                                      ttGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCtgat                     <  1:680269/139‑1 (MQ=255)                                                                                                      ttGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCtgat                     <  1:304470/139‑1 (MQ=255)                                                                                                      ttGTCTGCCTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCtgat                     <  2:223115/139‑1 (MQ=255)                                                                                                             ccTGTTGTTCTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCTGATGATAc                >  1:733083/1‑137 (MQ=255)                                                                                                                      cTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCa                                                                                            <  1:507061/52‑1 (MQ=255)                                                                                                                      cTGGCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCa                                                                                            >  2:507061/1‑52 (MQ=255)                                                                                                                         gCAGCTCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCTGATGATACCAGGATCAACTGGc  <  1:637828/139‑1 (MQ=255)                                                                                                                              |                                                                                                                                      TGTCGTCCGTATTGCCGATTTAATATTGAGCATTGCGTAAAAAAAATATCACTGGATACATTATGGTACCCTCAACATTTTCTC‑GTTTGAAAGCCGCGCGTTGTCTGCCTGTTGTTCTGGCAGCCCTGATTTTCGCCGGTTGTGGCACCCATACTCCCGATCAGTCCACTGCTTATATGCAGGGCACGGCGCAGGCTGATTCTGCCTTTTATCTTCAGCAGATGCAGCAAAGCTCTGATGATACCAGGATCAACTGGC  >  NZ_CP009273/3286697‑3286954

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑