Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,060	A→G	G392G (GGT→GGC)	intR ←	Rac prophage; putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,060	0	A	G	100.0%	225.0 / NA	61	G392G (GGT→GGC)	intR	Rac prophage; putative integrase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (32/29);  total (32/29)

GTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCA  >  NC_000913/1411926‑1412195                                                                                                                                       |                                                                                                                                        gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTa                                                                                                                                    >  2:930946/1‑140 (MQ=255)  tAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAAGCCACATGCCGTaa                                                                                                                                   <  2:279801/140‑1 (MQ=255)    aTTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAAt                                                                                                                                 <  2:935102/140‑1 (MQ=255)      ttgttgATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAAttt                                                                                                                               <  1:707200/140‑1 (MQ=255)          tgATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATa                                                                                                                           >  1:7652/1‑140 (MQ=255)                tCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCAt                                                                                                                     <  2:431291/140‑1 (MQ=255)                tCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCAt                                                                                                                     <  1:173208/140‑1 (MQ=255)                     cATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTgcg                                                                                                                <  2:993782/140‑1 (MQ=255)                       ttattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCa                                                                                                              <  2:154380/140‑1 (MQ=255)                                  ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTgcg                                                                                                                <  2:652411/127‑1 (MQ=255)                                  ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTgcg                                                                                                                >  1:652411/1‑127 (MQ=255)                                    ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCa                                                                                                 >  1:911179/1‑140 (MQ=255)                                          cTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc                                                                                           <  1:518667/140‑1 (MQ=255)                                          cTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc                                                                                           >  2:303202/1‑140 (MQ=255)                                             aaTGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctgg                                                                                        >  1:663336/1‑140 (MQ=255)                                               tGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctggc                                                                                       <  1:1181311/139‑1 (MQ=255)                                               tGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctggc                                                                                       >  2:1181311/1‑139 (MQ=255)                                               tGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTggctggct                                                                                      >  1:235721/1‑140 (MQ=255)                                               tGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTggctggct                                                                                      >  2:85467/1‑140 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            >  2:180170/1‑132 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            <  2:196984/132‑1 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            <  2:1163084/132‑1 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            >  1:196984/1‑132 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            <  1:180170/132‑1 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            >  1:1163084/1‑132 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtat                                                                                    >  1:599998/1‑140 (MQ=255)                                                 gggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtat                                                                                    <  1:930946/140‑1 (MQ=255)                                                  ggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtata                                                                                   >  1:538539/1‑140 (MQ=255)                                                  ggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtata                                                                                   >  1:535307/1‑140 (MQ=255)                                                  ggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtata                                                                                   >  1:876922/1‑140 (MQ=255)                                                  ggCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTAGCTGGCtata                                                                                   >  1:1148908/1‑140 (MQ=255)                                                       aTTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            <  1:1119219/126‑1 (MQ=255)                                                       aTTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                                                                                            >  2:1119219/1‑126 (MQ=255)                                                                       gCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGcc                                                              >  2:329591/1‑140 (MQ=255)                                                                          aCTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTc                                                           >  1:378249/1‑140 (MQ=255)                                                                                  aaCCCCGCTTTCAACATGGTTTTTTTTTCGCCGTTTGTGTCATTACGCCACAGGCCGTAAATTTCATACACCACCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagcca                                                   <  2:911179/140‑1 (MQ=255)                                                                                   aCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagccag                                                  <  2:281395/140‑1 (MQ=255)                                                                                   aCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagccag                                                  <  1:85467/140‑1 (MQ=255)                                                                                   aCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagccag                                                  <  2:7652/140‑1 (MQ=255)                                                                                     cgcgCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCcagca                                                >  2:861426/1‑140 (MQ=255)                                                                                       cgcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAgg                                              >  2:1098651/1‑140 (MQ=255)                                                                                       cgcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAgg                                              >  2:1080233/1‑140 (MQ=255)                                                                                       cgcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAgg                                              >  1:861377/1‑140 (MQ=255)                                                                                       cgcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAgg                                              <  2:873766/140‑1 (MQ=255)                                                                                        gcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGc                                             <  2:434943/140‑1 (MQ=255)                                                                                                 aTGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATg                                    <  2:1148908/140‑1 (MQ=255)                                                                                                   ggCTATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGcc                                  <  1:1098651/140‑1 (MQ=255)                                                                                                      tATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTAt                                     >  2:78759/1‑134 (MQ=255)                                                                                                      tATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTAt                                     <  1:78759/134‑1 (MQ=255)                                                                                                      tATCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCcgcg                               >  2:293480/1‑140 (MQ=255)                                                                                                       aTCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGt                              <  2:644287/140‑1 (MQ=255)                                                                                                        tttGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTa                             <  1:861426/138‑1 (MQ=255)                                                                                                        tCTGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTa                             <  2:378249/140‑1 (MQ=255)                                                                                                          tGTTCGTCGTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATg                           >  2:554969/1‑140 (MQ=255)                                                                                                             tcgtcgTTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGCTa                        <  1:329591/140‑1 (MQ=255)                                                                                                              cgtcgtTCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTAc                       >  2:1205565/1‑140 (MQ=255)                                                                                                                    tCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTa                        >  2:531754/1‑133 (MQ=255)                                                                                                                    tCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTa                        <  1:531754/133‑1 (MQ=255)                                                                                                                    tCATGTCATCAATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTa                 >  2:444134/1‑140 (MQ=255)                                                                                                                           atcaATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACggcggc          >  1:1214880/1‑140 (MQ=255)                                                                                                                             caATCCACATGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGa        >  2:867659/1‑140 (MQ=255)                                                                                                                                   acaTGCCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCa  <  2:663336/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                        GTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCA  >  NC_000913/1411926‑1412195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑