Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,200,747	A→G	S20S (AGT→AGC)	intE ←	e14 prophage; putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,200,747	0	A	G	100.0%	206.3 / NA	55	S20S (AGT→AGC)	intE	e14 prophage; putative integrase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/27);  total (28/27)

TGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTACTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCG  >  NC_000913/1200610‑1200883                                                                                                                                          |                                                                                                                                         tGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGCTAGCTTCAGCGTCGGTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGGCTAAAGTTACCTTCctgct                                                                                                                                        >  2:1496892/1‑140 (MQ=255)      gtttCTTTGTTCAGCCGGGCGAGTGTGGGCCTCAGTGGCAATGGCGATAGTTTCAGTTTCGTTTTTCCCAAAAGCATGAAATTTTCCTTTCCCTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATaaa                                                                                                                                   <  2:1302912/138‑1 (MQ=255)       gTTTTTTGTGCAGCCGGGTGAGTGTTGCCCTAAGAGGAAAGCGAGATATGTTCAGCTTGGTTTGTTCCCAAAGCATGGAATTTCCCTGTCACTGGATGCTAATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAg                                                                                                                                  <  2:232223/140‑1 (MQ=255)        ttCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGc                                                                                                                                 >  2:1289557/1‑140 (MQ=255)        ttCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGc                                                                                                                                 <  2:509031/140‑1 (MQ=255)            ttGTTCAGCCGGGCGGGTGTGGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTTTTCCCAAAGCATGAAATTTTCCTGTCACTGGAGGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGat                                                                                                                             <  2:653729/140‑1 (MQ=255)            ttGTTCAGCCAGGCGGGTGTTGGCCTCGGTGGCAATAGCGATAGCTTCAGCTTCTTTTGTCCCCAAAGCATGAAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGat                                                                                                                             <  2:1174173/140‑1 (MQ=255)            ttGTCCAGCCGGGCGGGTGTGGGCCTCAGTGGAAATAGCGATAGTTTCAGTTTCTTTTGTCCCAAAAGCATGGATTTTTCCTGTCCCGGGATGTTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGat                                                                                                                             <  2:1454052/140‑1 (MQ=255)                       ggCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAggg                                                                                                                  >  1:389113/1‑140 (MQ=255)                       ggCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAggg                                                                                                                  >  1:400068/1‑140 (MQ=255)                        gCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGa                                                                                                                 <  1:1067194/140‑1 (MQ=255)                        gCGAGTGTTGGCCTCAGGGGCAATTCCGATGGCTTCATCTTTGTTTTTTCCCAAAGAATGTAATTTTCCTTACACGGGGTGCTTATTCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGa                                                                                                                 <  2:251244/140‑1 (MQ=255)                            gtgtTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCAAAAGCATGGATTTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGa                                                                                                             <  1:429174/140‑1 (MQ=255)                             tgtTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGaa                                                                                                            >  1:991984/1‑140 (MQ=255)                              gtTGCCCTCAGTGGAAATAGCGATAGCTTAAGCTTCGTTTGTCCCAAAAGCATGGATTTTTCCTGTCACTGGATGTTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGaaa                                                                                                           <  2:1426688/140‑1 (MQ=255)                                gggCCTCAGGGGCAATAGCGATAGCTCCAGCTTCGTTTGTTCCAAAAGCATGGATTTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACa                                                                                                         <  2:160185/139‑1 (MQ=255)                                       aGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCt                                                                                                  >  1:60939/1‑140 (MQ=255)                                          ggCAATAGCAATGGCTTCAGTTTCGTTTGTCCCCAAAGCATGGATTTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTAc                                                                                               <  2:222726/140‑1 (MQ=255)                                            cAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTAcgc                                                                                             >  1:11480/1‑140 (MQ=255)                                            cAATAGCGATACTTTCGGTTTCGTTTGTTCCCAAAGCATGGATTTTTCCTGTCGCTGGTTGTTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTAcgc                                                                                             <  2:149989/140‑1 (MQ=255)                                               tAGCGATAGCTTCAGCTTCGTTTGTCCCAAAAGCATGGAATTTTCCTGTCACGGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGt                                                                                          <  1:787060/140‑1 (MQ=255)                                                        cttcagcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGcc                                                                                 >  2:1087197/1‑140 (MQ=255)                                                           cagcttcGTTTGTTCCCAAAGCATGAATTTTTCCTGTCACTGGATGTTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCAtt                                                                              <  1:16088/140‑1 (MQ=255)                                                                  gTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTAATCTTACGCGGTCTGGCTGCCATTACTCaaa                                                                       >  2:230185/1‑140 (MQ=255)                                                                   tttGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCaaaa                                                                      >  1:1131877/1‑140 (MQ=255)                                                                   tttGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCaaaa                                                                      >  1:1430505/1‑140 (MQ=255)                                                                      gtccccAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATcc                                                                   <  1:558392/137‑1 (MQ=255)                                                                                 aTGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGt                                                        >  2:853725/1‑140 (MQ=255)                                                                                  tGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTa                                                       >  1:773042/1‑140 (MQ=255)                                                                                                  cTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCtt                                       <  1:886278/140‑1 (MQ=255)                                                                                                  cTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCtt                                       <  1:1289557/140‑1 (MQ=255)                                                                                                      aggtttttaCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCA‑TACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTa                                  <  2:400068/133‑1 (MQ=255)                                                                                                      aTGCTTATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCA‑TACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTa                                  <  2:389113/140‑1 (MQ=255)                                                                                                        gtttATACCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTAc                                 <  1:1496892/138‑1 (MQ=255)                                                                                                           tataCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAgg                              >  2:1299144/1‑140 (MQ=255)                                                                                                           tataCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAgg                              >  2:753004/1‑140 (MQ=255)                                                                                                            ataCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGgt                             >  2:1193543/1‑140 (MQ=255)                                                                                                             taCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGgtg                            <  2:1105370/140‑1 (MQ=255)                                                                                                             taCCGCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGgtg                            >  1:797424/1‑140 (MQ=255)                                                                                                                 gCCAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAc                        >  2:819492/1‑140 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       >  1:573727/1‑140 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       >  1:1306821/1‑140 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       >  2:51843/1‑140 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       <  2:60939/140‑1 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       >  1:1270481/1‑140 (MQ=255)                                                                                                                  ccAATAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTCCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTAcc                       >  2:1243066/1‑140 (MQ=255)                                                                                                                    aaTAGACTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGACATTTATCTTGATGACAGGTGTTACCaa                     >  2:1359690/1‑140 (MQ=255)                                                                                                                          cTTTATTTACCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTcccc               >  1:1518979/1‑140 (MQ=255)                                                                                                                               tttaCCTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCaacta          >  2:741931/1‑140 (MQ=255)                                                                                                                                    cTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCg     <  1:819492/140‑1 (MQ=255)                                                                                                                                    cTTCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCg     <  1:1087197/140‑1 (MQ=255)                                                                                                                                     ttCCTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCgg    >  1:10853/1‑140 (MQ=255)                                                                                                                                       ccTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCg  <  2:474326/140‑1 (MQ=255)                                                                                                                                       ccTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCg  <  2:773042/140‑1 (MQ=255)                                                                                                                                       ccTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCg  >  2:1077722/1‑140 (MQ=255)                                                                                                                                       ccTGCTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCg  >  2:1222541/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                         TGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTACTATAAAGCGGATATAAGTTAGGGACTGAAACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTCATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCG  >  NC_000913/1200610‑1200883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑