Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	316,465	T→C	pseudogene (672/687 nt)	ykgA ←	putative DNA‑binding transcriptional regulator YkgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	316,465	0	T	C	100.0%	211.1 / NA	59	pseudogene (672/687 nt)	ykgA	putative DNA‑binding transcriptional regulator YkgA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (26/33);  total (26/33)

GGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTGGAAA  >  NC_000913/316348‑316601                                                                                                                      |                                                                                                                                         ggCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATaaa                                                                                                                    <  1:1192174/140‑1 (MQ=18)    aaCGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTc                                                                                                                 >  2:690068/1‑140 (MQ=25)       ggTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTc                                                                                                              <  1:690068/140‑1 (MQ=255)          gtTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCggg                                                                                                           <  1:925428/140‑1 (MQ=255)                   tatCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGttc                                                                                                  >  2:1191194/1‑138 (MQ=255)                   tatCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  >  1:569710/1‑140 (MQ=255)                   tatCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  >  2:635989/1‑140 (MQ=255)                   tatCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  >  1:980323/1‑140 (MQ=255)                    atCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCa                                                                                                 <  1:635989/140‑1 (MQ=255)                        aaTGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCCCTTCGGAAGAAATTGAAAACAAGAACCTCGCTTAGGCCCGTGTCCGCATTACGTGGGGAGGATCCTAAAGTCCCCGGGGCGTTGGCCAccct                                                                                             >  2:459010/1‑140 (MQ=14)                        aaTGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCActct                                                                                             >  2:1038383/1‑140 (MQ=255)                         aTGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCtt                                                                                            >  1:616788/1‑140 (MQ=255)                          tgtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  >  2:1139421/1‑133 (MQ=255)                          tgtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  <  1:1139421/133‑1 (MQ=255)                          tgtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCttt                                                                                           >  2:960936/1‑140 (MQ=255)                          tgtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCttt                                                                                           >  2:283147/1‑140 (MQ=255)                           gtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCtttt                                                                                          >  2:684670/1‑140 (MQ=255)                             gATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGGATAATTTGAAAACAAGAACCTCGCTTTGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGGCGGTGTGCACTCTTTTgg                                                                                        >  2:1215529/1‑140 (MQ=17)                                 aCAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATg                                                                                    <  1:960936/140‑1 (MQ=255)                                   aaTCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  >  1:1134421/1‑124 (MQ=255)                                   aaTCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTcc                                                                                                  <  2:1134421/124‑1 (MQ=255)                                   aaTCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTc                                                                                  <  1:1038383/140‑1 (MQ=255)                                     tCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGt                                                                                   >  1:556186/1‑137 (MQ=255)                                     tCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGt                                                                                   <  2:556186/137‑1 (MQ=255)                                     tCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAg                                                                                >  2:27579/1‑140 (MQ=255)                                     tCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAg                                                                                <  1:1215529/140‑1 (MQ=255)                                     tCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAg                                                                                <  1:788549/140‑1 (MQ=255)                                      cGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGc                                                                               <  2:922281/140‑1 (MQ=255)                                      cGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGc                                                                               <  2:548834/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  1:27579/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  1:65711/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  1:283147/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  2:569710/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  2:616788/140‑1 (MQ=255)                                       ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCa                                                                              <  2:647494/140‑1 (MQ=255)                                        gTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCat                                                                             <  1:166235/140‑1 (MQ=255)                                        gTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCat                                                                             <  1:321659/140‑1 (MQ=255)                                        gTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCat                                                                             >  1:780373/1‑140 (MQ=255)                                                 gcACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCat                                                                             >  1:265613/1‑131 (MQ=255)                                                 gcACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCat                                                                             <  2:265613/131‑1 (MQ=255)                                                     aGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACAt                                                                     >  1:155719/1‑135 (MQ=255)                                                     aGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACAt                                                                     <  2:155719/135‑1 (MQ=255)                                                        tGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTAcc                                                             <  2:980323/140‑1 (MQ=255)                                                         ggTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCa                                                            >  1:760120/1‑140 (MQ=255)                                                            gtgGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCa                                                         >  1:329636/1‑140 (MQ=255)                                                               gcggcCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTca                                                                        <  2:741590/122‑1 (MQ=255)                                                               gcggcCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTca                                                                        >  1:741590/1‑122 (MQ=255)                                                                 ggcCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGt                                                    >  2:966014/1‑140 (MQ=255)                                                                        gTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAAcc                                             <  1:934677/140‑1 (MQ=255)                                                                         tCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCg                                            <  2:329636/140‑1 (MQ=255)                                                                                      gAAAACAAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGAc                               <  1:966014/140‑1 (MQ=255)                                                                                             aGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGAtttt                        >  2:232012/1‑140 (MQ=255)                                                                                                 ccTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTttgttg                    <  2:1152681/140‑1 (MQ=255)                                                                                                  cTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGa                   <  1:573771/140‑1 (MQ=255)                                                                                                    cGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACg                 >  1:159993/1‑140 (MQ=255)                                                                                                         aGGCCTGTGTCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCa            >  2:216177/1‑140 (MQ=255)                                                                                                               gtgtCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTg      >  1:962769/1‑140 (MQ=255)                                                                                                                 gtCCACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTGGa    <  1:232012/140‑1 (MQ=255)                                                                                                                   ccACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTGGaaa  <  1:459010/140‑1 (MQ=255)                                                                                                                   ccACATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTGGaaa  <  2:780373/140‑1 (MQ=255)                                                                                                                      |                                                                                                                                         GGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCATAAAGTCCTCGGGTCGTTGTCCACTCTTTTGGCATGTCAGCATATTCACATACCGTACCAGCAAAAGTTTCAACCGTGAGCAAATCGACCGATTTTGTTGACGGTTCAAACGTGGAAA  >  NC_000913/316348‑316601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑