Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	393,709	A→G	pseudogene (740/1449 nt)	yaiT →	putative autotransporter YaiT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	393,709	0	A	G	100.0%	186.8 / NA	53	pseudogene (740/1449 nt)	yaiT	putative autotransporter YaiT
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/28);  total (25/28)

GGAACAAGACACCGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAACGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGCCTAC  >  NC_000913/393575‑393845                                                                                                                                       |                                                                                                                                         ggaacAAGACACCGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACGTCAACGGCGACAGCGGCACCATCAAATATGCTCAGGATGTTAGCGGca                                                                                                                                     >  2:299313/1‑140 (MQ=255)  gaacAAGACACCGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGcat                                                                                                                                    <  2:74767/140‑1 (MQ=255)          cacCGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCg                                                                                                                            <  2:111370/140‑1 (MQ=255)             cGTTGGTACTCGTCTGACCAACTCTCGTCGTGGCCTGCCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGgtg                                                                                                                         <  1:299313/140‑1 (MQ=255)             cGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATGAACTATGGTCAGGAGGTTAGCGGCATCATGGTCGgtg                                                                                                                         >  1:249316/1‑140 (MQ=255)             cGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGCAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGgtg                                                                                                                         >  2:102045/1‑140 (MQ=255)               ttGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGtt                                                                                                                       <  1:35502/140‑1 (MQ=255)                   tACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATa                                                                                                                   <  2:442438/140‑1 (MQ=255)                       cGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTGAGCAGCGTCATGGACGGTGTTGATACCaa                                                                                                               >  1:259704/1‑140 (MQ=255)                       cGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCAGCAACTATGGTCATGATCTTAGCGGCGTCATAGTCGGTGTTGATACCaa                                                                                                               >  2:308708/1‑140 (MQ=255)                           tGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAAtt                                                                                                           <  1:718017/140‑1 (MQ=255)                            gACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTg                                                                                                          >  2:73892/1‑140 (MQ=255)                              ccAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGAc                                                                                                        <  2:485987/140‑1 (MQ=255)                                  ctctCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACTGCGACAACGGCACCATCAACTATGATTAGGATGTTGGCGGCATCATGGTCGGAGTTGATACCAAAATTGACGGTa                                                                                                    >  2:325983/1‑140 (MQ=255)                                   tctcGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaa                                                                                                   <  1:73892/140‑1 (MQ=255)                                   tctcGTCATGGCCTGACTGATACCGCCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaa                                                                                                   <  1:239875/140‑1 (MQ=255)                                       gTCATGGCCTGGCTGATAACGGCGGCGGATTGGTGAGCTACTTCGGGGGGAACTTCAACGGCGACCACAGCACCATCAACTATGATCAGGATGTTAGCGGCATCTTGGTCGGTGTTGATACCAAAATTGACGGTaacaac                                                                                               >  2:528624/1‑140 (MQ=255)                                       gTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaacaac                                                                                               >  2:626422/1‑140 (MQ=255)                                       gTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaacaac                                                                                               >  1:596723/1‑140 (MQ=255)                                        tCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACg                                                                                              <  1:558849/140‑1 (MQ=255)                                          aTGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCt                                                                                            <  1:653996/140‑1 (MQ=255)                                               cTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTg                                                                                       >  1:102202/1‑140 (MQ=255)                                                 ggCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaa                                                                                                   >  2:411767/1‑126 (MQ=255)                                                 ggCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTaa                                                                                                   <  1:411767/126‑1 (MQ=255)                                                  gCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGc                                                                                             >  1:748031/1‑131 (MQ=255)                                                  gCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGc                                                                                             <  2:748031/131‑1 (MQ=255)                                                  gCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGAt                                                                                    >  1:511958/1‑140 (MQ=255)                                                  gCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGAt                                                                                    >  1:809546/1‑140 (MQ=255)                                                                cgcATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGGTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTg                                                                      >  2:410132/1‑140 (MQ=255)                                                                     gggTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGc                                                                 <  2:640936/140‑1 (MQ=255)                                                                            cTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTa                                                          >  1:11265/1‑140 (MQ=255)                                                                              aCTTCGGTGGTAACTTCTACGGCGACAACGGCACCTTCAGCTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTaaa                                                        <  2:249316/140‑1 (MQ=255)                                                                              aCTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTaaa                                                        <  1:626422/140‑1 (MQ=255)                                                                               cTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGAGCGTGGGGGCGGCTGCAGGCTTCGCTAAAg                                                       >  1:263859/1‑140 (MQ=255)                                                                                 tCGGTGGTAACTTCAACGGCGATAACGGCACCATCCACTCTGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGt                                                     <  2:263859/140‑1 (MQ=255)                                                                                 tCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGt                                                     >  2:795342/1‑140 (MQ=255)                                                                                            ttCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACatgaatga                                          <  2:809546/140‑1 (MQ=255)                                                                                                          cGGCACCATCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAgg                            <  2:511958/140‑1 (MQ=255)                                                                                                                  tCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTgg                                 <  1:167545/127‑1 (MQ=255)                                                                                                                  tCAACTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTgg                                 >  2:167545/1‑127 (MQ=255)                                                                                                                     aCTATGATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGAc                 >  2:24564/1‑140 (MQ=255)                                                                                                                          gATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGAGCGTCCTGGTCAGGGGGATCAAGACAGCCa            >  1:261741/1‑140 (MQ=255)                                                                                                                          gATCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCa            >  2:416771/1‑140 (MQ=255)                                                                                                                           aTCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAg           <  2:102202/140‑1 (MQ=255)                                                                                                                            tCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGa          <  1:502245/140‑1 (MQ=255)                                                                                                                            tCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGa          >  1:556858/1‑140 (MQ=255)                                                                                                                            tCAGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGa          <  2:556858/140‑1 (MQ=255)                                                                                                                            tCAGGATGTTAGCGGCATCATGATCAGTGCTGATACCCAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCATGACAGCCAGa          <  1:388807/140‑1 (MQ=255)                                                                                                                            tCAGGATGTTAGCGGCAACATGGTCGGTGTTGATAGCAACATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGa          <  2:261741/140‑1 (MQ=255)                                                                                                                              aGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGc              <  2:425667/134‑1 (MQ=255)                                                                                                                              aGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGc              >  1:425667/1‑134 (MQ=255)                                                                                                                              aGGATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACt        >  1:533492/1‑140 (MQ=255)                                                                                                                                gATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATAACCGTTCTGGTCAGTTGGATCAAGACAGCCAGACTGc      >  1:315440/1‑140 (MQ=255)                                                                                                                                gATGTTAGCGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGCTGACATGACTGAACGTTGTGGTCAGGTGGATCATGACAGCCAGACTGc      >  2:388807/1‑140 (MQ=255)                                                                                                                                 aTGTTAGCGGCATCATTGTCGGTGTTGATACCAAATTTGACGGTAACAGCGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGcc     <  2:370428/140‑1 (MQ=255)                                                                                                                                 aTGTTAGCGGCATCACGGTCGGTGTCGATCCCAAAATGGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGcc     <  1:308708/140‑1 (MQ=255)                                                                                                                                    ttAGCGGCTTCATGGTCGGTGTCGATACCACGAATTACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGCCTAc  <  2:388923/140‑1 (MQ=255)                                                                                                                                    ttAGCGGCATCATGGTCTGTGTTGATACCAATATTAACGTTAACAACGTTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGCCTAc  <  2:315440/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                         GGAACAAGACACCGTTGGTACTCGTCTGACCAACTCTCGTCATGGCCTGGCTGATAACGGCGGCGCATGGGTAAGCTACTTCGGTGGTAACTTCAACGGCGACAACGGCACCATCAACTATGATCAGGATGTTAACGGCATCATGGTCGGTGTTGATACCAAAATTGACGGTAACAACGCTAAGTGGATCGTCGGTGCGGCTGCAGGCTTCGCTAAAGGTGACATGAATGACCGTTCTGGTCAGGTGGATCAAGACAGCCAGACTGCCTAC  >  NC_000913/393575‑393845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑