Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,673,624	C→T	intergenic (‑123/‑289)	mdtJ ← / → tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,673,624	0	C	T	100.0%	206.2 / NA	63	intergenic (‑123/‑289)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/32);  total (31/32)

ATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCCAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTCGTCATCGCGGATGATAA  >  NC_000913/1673490‑1673757                                                                                                                                       |                                                                                                                                      ataaataTACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGtg                                                                                                                                   <  1:1380819/139‑1 (MQ=255)      tataCATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTgctgct                                                                                                                              <  1:478740/139‑1 (MQ=255)       ataCATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTc                                                                                                                             >  2:264962/1‑139 (MQ=255)           aTTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCt                                                                                                                         <  1:264962/139‑1 (MQ=255)           aTTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCt                                                                                                                         <  1:192624/139‑1 (MQ=255)             tGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCt                                                                                                                         <  1:740977/137‑1 (MQ=255)             tGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCt                                                                                                                         >  2:740977/1‑137 (MQ=255)              gTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACg                                                                                                                      >  1:3636/1‑139 (MQ=255)               tCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGa                                                                                                                     >  1:583410/1‑139 (MQ=255)                    ctcCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAg                                                                                                                >  1:1091699/1‑139 (MQ=255)                         gCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGt                                                                                                           >  2:1566981/1‑139 (MQ=255)                         gCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGt                                                                                                           >  1:1366409/1‑139 (MQ=255)                           aaGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTgg                                                                                                         <  2:583410/139‑1 (MQ=255)                             gagaATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGAt                                                                                                       <  2:1366409/139‑1 (MQ=255)                             gagaATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGAt                                                                                                       <  2:1091699/139‑1 (MQ=255)                               gaATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGa                                                                                                     >  1:325723/1‑139 (MQ=255)                                 attattTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAgg                                                                                                   >  2:748582/1‑139 (MQ=255)                                          aTTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      >  2:267161/1‑127 (MQ=255)                                          aTTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      <  1:267161/127‑1 (MQ=255)                                             ttCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATggg                                                                                       <  2:3636/139‑1 (MQ=255)                                               cGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGtg                                                                                                                                   <  2:310352/93‑1 (MQ=255)                                               cGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGtg                                                                                                                                   >  1:310352/1‑93 (MQ=255)                                                    aaTTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGAt                                                                                                              <  1:1474088/109‑1 (MQ=255)                                                    aaTTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGAt                                                                                                              >  2:1474088/1‑109 (MQ=255)                                                    aaTTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGt                                                                                <  1:748582/139‑1 (MQ=255)                                                           cGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      <  1:381016/110‑1 (MQ=255)                                                           cGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      >  2:381016/1‑110 (MQ=255)                                                                ccAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      <  1:556053/105‑1 (MQ=255)                                                                ccAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      >  2:556053/1‑105 (MQ=255)                                                                          gtGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACaaa                                                          <  1:184022/139‑1 (MQ=255)                                                                           tGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAg                                                                                                                    <  2:633841/80‑1 (MQ=255)                                                                           tGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAg                                                                                                                    >  1:633841/1‑80 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGa                                                                                                               <  1:854879/83‑1 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGa                                                                                                               >  2:854879/1‑83 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      <  1:719285/92‑1 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATg                                                                                                      >  2:719285/1‑92 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGa                                                                                              >  1:626586/1‑100 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGa                                                                                              <  2:626586/100‑1 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTg                                                       >  1:953283/1‑139 (MQ=255)                                                                             gTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTg                                                       >  2:244981/1‑139 (MQ=255)                                                                                aaGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACaaa                                                          >  1:890982/1‑133 (MQ=255)                                                                                aaGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACaaa                                                          <  2:890982/133‑1 (MQ=255)                                                                                 aGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCa                                                   <  2:953283/139‑1 (MQ=255)                                                                                 aGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCa                                                   <  2:325723/139‑1 (MQ=255)                                                                                       gcgcATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGt                                                                                      >  2:132049/1‑98 (MQ=255)                                                                                       gcgcATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGt                                                                                      <  1:132049/98‑1 (MQ=255)                                                                                       gcgcATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAatat                                             <  2:326619/139‑1 (MQ=255)                                                                                       gcgcATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAatat                                             >  1:228851/1‑139 (MQ=255)                                                                                                  aaGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGa                                                                                           <  1:1244761/82‑1 (MQ=255)                                                                                                  aaGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGa                                                                                           >  2:1244761/1‑82 (MQ=255)                                                                                                   aGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCg                                 <  1:1566981/139‑1 (MQ=255)                                                                                                         ggCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCa                                                   >  2:206106/1‑115 (MQ=255)                                                                                                         ggCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCa                                                   <  1:206106/115‑1 (MQ=255)                                                                                                         ggCAGAAGAAAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAgtgt                           <  1:244981/139‑1 (MQ=255)                                                                                                                gaaAGGACTAAAGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTtct                    >  1:1322437/1‑139 (MQ=255)                                                                                                                          aaGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGAt                                                                                                       <  2:897423/46‑1 (MQ=255)                                                                                                                          aaGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACaaa                                                          >  2:1123655/1‑91 (MQ=255)                                                                                                                          aaGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACaaa                                                          <  1:1123655/91‑1 (MQ=255)                                                                                                                          aaGCGCGTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTCGTCATcgcg          <  2:1322437/139‑1 (MQ=255)                                                                                                                          aaGCGCGTTGCGCTAGTGATGCTCACCTACGAGCAAGATAGTGGAt                                                                                                       >  1:897423/1‑46 (MQ=255)                                                                                                                               cgTTGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTCGTCATCGCGgatga     >  2:388856/1‑139 (MQ=255)                                                                                                                                  tGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTTGTCATCGCGGATGATaa  >  2:780883/1‑139 (MQ=255)                                                                                                                                  tGCGCTAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTCGTCATCGCGGATGATaa  >  2:259487/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                      ATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAGCCCCGCGCATAGCGCAAGCTTTGGCAGAAGAAAGGACTAAAGCGCGTTGCGCCAGTGCTGCTCACCTACGAGCAAGATAGTGGATGAGGTACGAAGATGGGTAAATGTAGAAAATAACGTCCTGAACAAATTGTCCATAATATTACAATTATCCGCAGTGTTGCTTCTCGTCATCGCGGATGATAA  >  NC_000913/1673490‑1673757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑