Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,527,388	T→C	intergenic (+236/‑502)	yncH → / → rhsE	DUF5445 domain‑containing protein YncH/RhsE protein in rhs element

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,527,388	0	T	C	100.0%	228.5 / NA	63	intergenic (+236/‑502)	yncH/rhsE	DUF5445 domain‑containing protein YncH/RhsE protein in rhs element
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (36/27);  total (36/27)

TATTCAAGAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGTACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGTGAAT  >  NC_000913/1527261‑1527511                                                                                                                                |                                                                                                                            tATTCAAGCAAATGGTTGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCActct                                                                                                                        <  1:287912/133‑1 (MQ=255)  aTTCAAGAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCtt                                                                                                                       >  1:503277/1‑133 (MQ=255)  aTTCAAGAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCtt                                                                                                                       >  2:450614/1‑133 (MQ=255)       aGAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCAc                                                                                                                  <  1:450614/133‑1 (MQ=255)        gAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACt                                                                                                                 >  1:461908/1‑133 (MQ=255)             tGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGc                                                                                                            >  1:94378/1‑133 (MQ=255)             tGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGc                                                                                                            >  2:51164/1‑133 (MQ=255)                      tttAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGatcatc                                                                                                   <  1:108776/133‑1 (MQ=255)                               tGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAg                                                                                          >  1:23286/1‑133 (MQ=255)                                   tCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGACAACACCATTTTGGGAACAATGCATCAGGCTCTCTTACCACTGAAGCAAGATCATCCGGCACCAggtgg                                                                                      <  2:115792/133‑1 (MQ=255)                                       aaTATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAggtggtggt                                                                                  >  2:478935/1‑133 (MQ=255)                                          ataACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCa                                                                               <  1:478935/133‑1 (MQ=255)                                              ccTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGc                                                                           >  1:150664/1‑133 (MQ=255)                                               cTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGGGGTGGTGCAGTGCt                                                                          >  2:640116/1‑133 (MQ=255)                                                   tCAGTAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTgg                                                                      >  1:353272/1‑133 (MQ=255)                                                   tCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGgtggtggtg                                                                                 >  1:560192/1‑122 (MQ=255)                                                   tCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGgtggtggtg                                                                                 <  2:560192/122‑1 (MQ=255)                                                   tCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCa                                                                               >  2:515117/1‑124 (MQ=255)                                                   tCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCa                                                                               <  1:515117/124‑1 (MQ=255)                                                   tCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTgg                                                                      >  2:24409/1‑133 (MQ=255)                                                       tAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAAt                                                                  >  2:150633/1‑133 (MQ=255)                                                        aGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATg                                                                 >  1:637020/1‑133 (MQ=255)                                                          aTTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGt                                                               >  1:416383/1‑133 (MQ=255)                                                          aTTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGt                                                               <  2:23286/133‑1 (MQ=255)                                                            tATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTcc                                                             >  2:122508/1‑133 (MQ=255)                                                            tATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTcc                                                             >  1:97840/1‑133 (MQ=255)                                                            tATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTcc                                                             <  1:51164/133‑1 (MQ=255)                                                            tATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTcc                                                             >  1:137798/1‑133 (MQ=255)                                                              tCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTcccc                                                           >  2:372181/1‑133 (MQ=255)                                                                 aGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCg                                                        >  2:565801/1‑133 (MQ=255)                                                                 aGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCg                                                        >  2:355860/1‑133 (MQ=255)                                                                      gagCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGa                                                   >  1:624659/1‑133 (MQ=255)                                                                       agCTACACATTATTGTAGGGGCAGCGGACAACCCCATTTTGAGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAg                                                  <  2:167464/133‑1 (MQ=255)                                                                         cTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGtt                                                <  2:97840/133‑1 (MQ=255)                                                                            cacaTTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGTTTTGGAAGTGGCCCCCTCGGGGGAGTTGTc                                             >  1:235342/1‑133 (MQ=255)                                                                            cacaTTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTc                                             >  1:65945/1‑133 (MQ=255)                                                                            cacaTTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTc                                             >  2:408536/1‑133 (MQ=255)                                                                            cacaTTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTc                                             >  1:369719/1‑133 (MQ=255)                                                                            cacaTTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGATGGTGCAGCGCTTTGGCAATGGTCCCCTCGTGGGAGTTGTc                                             >  2:231473/1‑133 (MQ=255)                                                                                 tattGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCattat                                        >  1:145915/1‑133 (MQ=255)                                                                                 tattGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCattat                                        >  1:78610/1‑133 (MQ=255)                                                                                    tGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTAtttt                                     <  2:503277/133‑1 (MQ=255)                                                                                      gAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCt                                   <  2:416383/133‑1 (MQ=255)                                                                                       aGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTa                                  <  2:489883/133‑1 (MQ=255)                                                                                       aGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTa                                  <  2:461908/133‑1 (MQ=255)                                                                                         gggCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATg                                >  1:457389/1‑133 (MQ=255)                                                                                           gCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTTGAAATGGTTCCCGCGGGGGAGTTGTGATTAGTTTCTATGCt                              >  2:181504/1‑133 (MQ=255)                                                                                           gCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCGCTCGGGGGAGTTGTAATTATTTTCTATGCt                              >  1:285687/1‑133 (MQ=255)                                                                                           gCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCt                              <  1:150633/133‑1 (MQ=255)                                                                                            cAGGGGAAAACACCAATTTGGGAACAATGCATGAGGCACTCGTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTa                             <  2:235342/133‑1 (MQ=255)                                                                                               gggAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTAttt                          <  1:122508/133‑1 (MQ=255)                                                                                               gggAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTAttt                          <  2:369719/133‑1 (MQ=255)                                                                                                 gAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGc                        <  2:137798/133‑1 (MQ=255)                                                                                                 gAAAACACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGc                        <  1:14574/133‑1 (MQ=255)                                                                                                 gAAAACACCATTTTGCGACCAAAGCATCAGACACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGc                        <  1:181504/133‑1 (MQ=255)                                                                                                    aaCACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGc                        >  1:59828/1‑130 (MQ=255)                                                                                                    aaCACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGc                        <  2:59828/130‑1 (MQ=255)                                                                                                    aaCACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCtta                     <  1:583863/133‑1 (MQ=255)                                                                                                    aaCACCATTTTGGGAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCtta                     <  2:150664/133‑1 (MQ=255)                                                                                                         cATTTTGGAAACAATGCATCAGCCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATtata                <  1:231473/133‑1 (MQ=255)                                                                                                                ggAACAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATATTCTATGTTATTTGCTTATTACATtcatca         >  1:313584/1‑133 (MQ=255)                                                                                                                   aCAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGTGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGt      >  1:540698/1‑133 (MQ=255)                                                                                                                    cAATGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGTg     <  2:457389/133‑1 (MQ=255)                                                                                                                      aTGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGTGaa   >  2:452782/1‑133 (MQ=255)                                                                                                                       tGCATCAGGCACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGTGAAt  <  2:353272/133‑1 (MQ=255)                                                                                                                                |                                                                                                                            TATTCAAGAAAATGGATGTATTTTAAATGTTGATTCTTAATATAACCTAATCAATAGATTATCAAGTGAGAGCTACACATTATTGGAGGGGCAGGGGAAAACACCATTTTGGGAACAATGCATCAGGTACTCTTACCACTGAAGCAAGATCATCCGGCACCAGGTGGTGGTGCAGTGCTTTGGAAATGGTCCCCTCGGGGGAGTTGTCATTATTTTCTATGCTATTTGCTTATTATATTCATCAGGTGAAT  >  NC_000913/1527261‑1527511

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: ‑