Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	282,228	A→G	intergenic (‑245/‑50)	yagA ← / → yagE	CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	282,228	0	A	G	100.0%	148.2 / NA	41	intergenic (‑245/‑50)	yagA/yagE	CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/16);  total (25/16)

TCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAACGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCGGGCAC  >  NC_000913/282093‑282363                                                                                                                                        |                                                                                                                                        tCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaa                                                                                                                                     <  2:739817/140‑1 (MQ=255)  cTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaac                                                                                                                                    >  1:429974/1‑140 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  1:74285/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:899855/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  1:672212/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:460140/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  1:616945/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:497966/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:672757/140‑1 (MQ=255)   ttttCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:606563/140‑1 (MQ=255)      tCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTg                                                                                                                                <  2:96633/140‑1 (MQ=255)      tCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTg                                                                                                                                <  1:447972/140‑1 (MQ=255)        ccccTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGtt                                                                                                                              <  2:126566/140‑1 (MQ=255)           cTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCta                                                                                                                           >  1:551640/1‑140 (MQ=255)            tCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   >  1:826986/1‑131 (MQ=255)            tCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:483361/131‑1 (MQ=255)            tCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   <  2:826986/131‑1 (MQ=255)            tCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAagcgaacg                                                                                                                                   >  1:483361/1‑131 (MQ=255)                            agGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATg                                                                                                          >  1:208088/1‑140 (MQ=255)                              ggCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGAt                                                                                                        >  1:682420/1‑140 (MQ=255)                              ggCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGAt                                                                                                        >  1:366860/1‑140 (MQ=255)                               gCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGAtt                                                                                                       <  2:429974/140‑1 (MQ=255)                                   gggTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGc                                                                                                   <  1:918057/140‑1 (MQ=255)                                            gCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGAtc                                                                                          <  2:366860/140‑1 (MQ=255)                                              aaTATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGAtctc                                                                                        >  2:222322/1‑140 (MQ=255)                                               atatGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCa                                                                                       <  2:54534/140‑1 (MQ=255)                                                           gCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcg                                                                           >  2:511754/1‑140 (MQ=255)                                                             ttAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgcg                                                                         <  2:682420/140‑1 (MQ=255)                                                                             cccTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCa                                                         >  2:102186/1‑140 (MQ=255)                                                                                tctTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTc                                                      >  1:768979/1‑140 (MQ=255)                                                                                   tcccttccGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTcccc                                                   <  1:626299/140‑1 (MQ=255)                                                                                      cttccGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTg                                                >  2:237376/1‑140 (MQ=255)                                                                                        tccGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGtc                                              >  1:725229/1‑140 (MQ=255)                                                                                        tccGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGtc                                              >  2:476322/1‑140 (MQ=255)                                                                                           gATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTcc                                           <  1:476322/140‑1 (MQ=255)                                                                                              ttACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCa                                                         >  1:426994/1‑123 (MQ=255)                                                                                              ttACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCa                                                         <  2:426994/123‑1 (MQ=255)                                                                                                      ccTTGTTCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTAc                                <  1:970768/140‑1 (MQ=255)                                                                                                           ttCTGCGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTAccgccg                           >  1:508114/1‑140 (MQ=255)                                                                                                                cGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc                      >  2:674698/1‑140 (MQ=255)                                                                                                                cGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc                      >  1:444364/1‑140 (MQ=255)                                                                                                                cGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc                      <  2:768979/140‑1 (MQ=255)                                                                                                                cGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc                      >  1:298024/1‑140 (MQ=255)                                                                                                                cGTCATAGTATGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc                      >  2:220667/1‑140 (MQ=255)                                                                                                                         aTGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGAt             <  2:725229/140‑1 (MQ=255)                                                                                                                         aTGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGAt             <  1:511754/140‑1 (MQ=255)                                                                                                                          tGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATa            >  1:519039/1‑140 (MQ=255)                                                                                                                          tGATCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATa            >  1:488315/1‑140 (MQ=255)                                                                                                                            aTCGTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAg          >  1:706013/1‑140 (MQ=255)                                                                                                                               gTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGAt             <  1:238991/134‑1 (MQ=255)                                                                                                                               gTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGAt             >  2:238991/1‑134 (MQ=255)                                                                                                                               gTTAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCg       >  1:7179/1‑140 (MQ=255)                                                                                                                                ttAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCgg      >  1:535155/1‑140 (MQ=255)                                                                                                                                ttAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCgg      >  1:405784/1‑140 (MQ=255)                                                                                                                                ttAAATAAGCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCgg      >  2:835984/1‑140 (MQ=255)                                                                                                                                 taaataagCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCggg     <  2:298024/140‑1 (MQ=255)                                                                                                                                   aataagCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCGGGCa   <  2:405784/140‑1 (MQ=255)                                                                                                                                    ataagCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCGGGCAc  >  2:479407/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        TCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACCTCTCCTTGTTCTGCGTCATAGTATGATCGTTAAATAAACGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAAGCCGGGCAC  >  NC_000913/282093‑282363

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: ‑