Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	850,389	T→C	intergenic (‑292/‑61)	rhtA ← / → ompX	threonine and homoserine efflux system/outer membrane protein X

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	850,389	0	T	C	100.0%	232.4 / NA	66	intergenic (‑292/‑61)	rhtA/ompX	threonine and homoserine efflux system/outer membrane protein X
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (32/34);  total (32/34)

GAATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGACT  >  NC_000913/850256‑850524                                                                                                                                      |                                                                                                                                        gaatgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt                                                                                                                                    <  2:1224570/139‑1 (MQ=255)            aaaaCATGCGTAATACTTACGCAGTTCTCTGAAATAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  1:1063262/139‑1 (MQ=255)            aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  2:226094/139‑1 (MQ=255)            aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  1:278765/139‑1 (MQ=255)            aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  1:1628198/139‑1 (MQ=255)                   gCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATAGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  <  1:757103/139‑1 (MQ=255)                    cGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTaa                                                                                                                 <  1:134388/139‑1 (MQ=255)                           cTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAg                                                                                                          >  1:1505162/1‑139 (MQ=255)                             tACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGa                                                                                                        <  2:1265300/139‑1 (MQ=255)                              aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         >  2:1574635/1‑121 (MQ=255)                              aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  1:1574635/121‑1 (MQ=255)                                    ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAttt                                                                                                 >  1:1021959/1‑139 (MQ=255)                                    ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAttt                                                                                                 >  1:1474898/1‑139 (MQ=255)                                      ctctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGa                                                                                               >  2:890550/1‑139 (MQ=255)                                        ctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  1:449316/139‑1 (MQ=255)                                        ctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  2:1474898/139‑1 (MQ=255)                                                gTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTg                                                                                     >  2:381671/1‑139 (MQ=255)                                                               aTGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  <  1:1406870/95‑1 (MQ=255)                                                               aTGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  >  2:1406870/1‑95 (MQ=255)                                                                   aTAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                       <  1:854720/102‑1 (MQ=255)                                                                   aTAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                       >  2:854720/1‑102 (MQ=255)                                                                         gtgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  2:1088321/106‑1 (MQ=255)                                                                         gtgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             >  1:1088321/1‑106 (MQ=255)                                                                          tgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGt                                                           >  2:1321910/1‑139 (MQ=255)                                                                            tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  <  2:1237862/82‑1 (MQ=255)                                                                            tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  >  1:1237862/1‑82 (MQ=255)                                                                            tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCt                                                         >  2:333896/1‑139 (MQ=255)                                                                             aTGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                            >  1:492345/1‑135 (MQ=255)                                                                             aTGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                            <  2:492345/135‑1 (MQ=255)                                                                                   aCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa                                                  >  1:1458999/1‑139 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         >  2:1509879/1‑67 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                         <  1:1509879/67‑1 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  1:1234827/95‑1 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             >  2:1234827/1‑95 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCAc                                                 >  1:178930/1‑139 (MQ=255)                                                                                    cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATGTGAATCACATTTGAGGTGGTTATGAATGAAATTGCATGTCTTTCAGCAc                                                 >  2:1153699/1‑139 (MQ=255)                                                                                      ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  1:200481/93‑1 (MQ=255)                                                                                      ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             >  2:200481/1‑93 (MQ=255)                                                                                      ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                               >  2:1073026/1‑139 (MQ=255)                                                                                      ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                               >  1:1350956/1‑139 (MQ=255)                                                                                        cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGc                                             >  2:767990/1‑139 (MQ=255)                                                                                          gTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCg                                           <  2:178930/139‑1 (MQ=255)                                                                                                   aaTGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  <  2:1261548/59‑1 (MQ=255)                                                                                                   aaTGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             >  1:627551/1‑80 (MQ=255)                                                                                                   aaTGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  2:627551/80‑1 (MQ=255)                                                                                                   aaTGCCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  >  1:1261548/1‑59 (MQ=255)                                                                                                     tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  >  2:1279543/1‑57 (MQ=255)                                                                                                     tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                  <  1:1279543/57‑1 (MQ=255)                                                                                                     tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCt                                >  2:452814/1‑139 (MQ=255)                                                                                                        cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             >  1:1494796/1‑75 (MQ=255)                                                                                                        cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                             <  2:1494796/75‑1 (MQ=255)                                                                                                        cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGGGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTc                             >  1:1096684/1‑139 (MQ=255)                                                                                                          cGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAc                           <  1:1073026/139‑1 (MQ=255)                                                                                                          cGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAc                           <  1:74617/139‑1 (MQ=255)                                                                                                          cGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAc                           <  1:890550/139‑1 (MQ=255)                                                                                                           gTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAcc                          <  2:1458999/139‑1 (MQ=255)                                                                                                           gTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAcc                          <  1:1321910/139‑1 (MQ=255)                                                                                                                aCATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGATGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAgg                     <  2:1579232/139‑1 (MQ=255)                                                                                                                    cacaAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACt                 >  2:647524/1‑139 (MQ=255)                                                                                                                    cacaAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTAGGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACt                 >  1:128540/1‑139 (MQ=255)                                                                                                                       aaaTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTcc              <  1:1348958/139‑1 (MQ=255)                                                                                                                        aaTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCg             <  1:333896/139‑1 (MQ=255)                                                                                                                        aaTCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCg             <  1:647524/139‑1 (MQ=255)                                                                                                                            gcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGc         >  2:562371/1‑139 (MQ=255)                                                                                                                                  agTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTACTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAc   <  2:1096684/139‑1 (MQ=255)                                                                                                                                   gTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGACt  >  2:1155766/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                        GAATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGACT  >  NC_000913/850256‑850524

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: ‑