Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,775,097	G→A	intergenic (+76/‑448)	yfjW → / → ypjI	CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,775,097	0	G	A	100.0%	200.0 / NA	56	intergenic (+76/‑448)	yfjW/ypjI	CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/28);  total (28/28)

TATAAAATTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGGCTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAGCG  >  NC_000913/2774964‑2775225                                                                                                                                      |                                                                                                                                 tataAAATTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAg                                                                                                                            <  2:918786/140‑1 (MQ=255)  ataAAATTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGc                                                                                                                           >  2:778641/1‑140 (MQ=255)    aaaaTTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGt                                                                                                                         <  1:1406377/140‑1 (MQ=255)    aaaaTTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGt                                                                                                                         <  1:723403/140‑1 (MQ=255)       attcattcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGaa                                                                                                                      >  2:77184/1‑140 (MQ=255)          cattcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCg                                                                                                                   <  1:1232124/140‑1 (MQ=255)          cattcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCg                                                                                                                   <  2:75629/140‑1 (MQ=255)          cattcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCg                                                                                                                   <  1:798905/140‑1 (MQ=255)           attcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGTAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCgg                                                                                                                  <  2:236919/140‑1 (MQ=255)           attcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCgg                                                                                                                  >  2:498505/1‑140 (MQ=255)           attcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCgg                                                                                                                  >  1:969061/1‑140 (MQ=255)           attcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCgg                                                                                                                  <  1:802792/140‑1 (MQ=255)           attcattcTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCgg                                                                                                                  <  1:498505/140‑1 (MQ=255)                      cTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATAcc                                                                                                       <  2:1356248/140‑1 (MQ=255)                         tAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGc                                                                                                    <  1:200454/140‑1 (MQ=255)                         tAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGc                                                                                                    >  1:741891/1‑140 (MQ=255)                           aGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATAcc                                                                                                       <  2:296048/135‑1 (MQ=255)                           aGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATAcc                                                                                                       >  1:296048/1‑135 (MQ=255)                           aGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCtt                                                                                                  >  2:276343/1‑140 (MQ=255)                                 atgTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGt                                                                                            >  2:846763/1‑140 (MQ=255)                                 atgTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGt                                                                                            >  2:677556/1‑140 (MQ=255)                                         gaaAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGtttt                                                                                    <  1:807945/140‑1 (MQ=255)                                         gaaAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGtttt                                                                                    <  2:741891/140‑1 (MQ=255)                                         gaaAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGtttt                                                                                    <  1:682855/140‑1 (MQ=255)                                          aaaaTTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGttttt                                                                                   >  2:1394840/1‑140 (MQ=255)                                             aTTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTc                                                                                >  1:423931/1‑140 (MQ=255)                                                     ttGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCa                                                                        <  1:778641/140‑1 (MQ=255)                                                     ttGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCa                                                                        <  1:1394840/140‑1 (MQ=255)                                                            gCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACatat                                                                 <  1:276343/140‑1 (MQ=255)                                                               tttGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATAtt                                                              >  2:1128253/1‑140 (MQ=255)                                                                  ggCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTAcc                                                                          <  1:813999/125‑1 (MQ=255)                                                                  ggCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTAcc                                                                          >  2:813999/1‑125 (MQ=255)                                                                  ggCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTc                                                           >  1:795447/1‑140 (MQ=255)                                                                    cTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCtg                                                         <  2:795447/140‑1 (MQ=255)                                                                           tGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTa                                                  <  1:833947/140‑1 (MQ=255)                                                                           tGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTa                                                  <  2:268335/140‑1 (MQ=255)                                                                                  tttttATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCa                                           >  1:1230350/1‑140 (MQ=255)                                                                                             atttattAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCgg                                >  2:845289/1‑140 (MQ=255)                                                                                              tttattAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGt                               >  2:784988/1‑140 (MQ=255)                                                                                              tttattAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGt                               >  1:915447/1‑140 (MQ=255)                                                                                              tttattAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGt                               >  1:344187/1‑140 (MQ=255)                                                                                              tttattAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGt                               >  1:1308637/1‑140 (MQ=255)                                                                                                 attaAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGa                            <  2:1230350/140‑1 (MQ=255)                                                                                                  ttaAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGaa                           <  1:677556/140‑1 (MQ=255)                                                                                                           ccTAAGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGaa                  >  1:137454/1‑140 (MQ=255)                                                                                                               aGTTAAGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAatat              >  2:413510/1‑140 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATTCCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGaaa                          <  1:839250/123‑1 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGaaa                          >  2:839250/1‑123 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGa         <  2:416805/140‑1 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGa         >  2:103007/1‑140 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGa         >  1:416805/1‑140 (MQ=255)                                                                                                                    aGCCTGTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGa         >  1:299800/1‑140 (MQ=255)                                                                                                                         gTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAg    <  2:299800/140‑1 (MQ=255)                                                                                                                         gTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAg    <  1:103007/140‑1 (MQ=255)                                                                                                                         gTTTTTAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAg    >  1:1224247/1‑140 (MQ=255)                                                                                                                           ttttAAAGCAGACTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAGCg  >  1:985405/1‑140 (MQ=255)                                                                                                                                      |                                                                                                                                 TATAAAATTCATTCATTCTTACTTTAAGAATGATGTGAATGAAAATTTATTCTTGTAACGCATTTGGCTCCAATTGGAGCCTTTTTATGACTATTTATTAAAATATCCTAAGTTAAGCCTGTTTTTAAAGCAGGCTTGAGCGTGAAGCGGACACTCATACCTGCTTTAAAGTGGCGTTTTTGTCGTTACCCATACCTATATTTTCTGTTGTTTAACTGCCAGAACTGAGCGGTTGAAAAGCCAGAAATATGCCGAGCCAGCG  >  NC_000913/2774964‑2775225

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: ‑