Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,996,070	T→C	pseudogene (291/399 nt)	ygeO ←	putative uncharacterized protein YgeO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,996,070	0	T	C	100.0%	222.0 / NA	62	pseudogene (291/399 nt)	ygeO	putative uncharacterized protein YgeO
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/37);  total (25/37)

TTTCTTTCAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAT  >  NC_000913/2995933‑2996205                                                                                                                                          |                                                                                                                                        tttctttcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAACAGTGTTGATGCAAGTGGTAACGGCGATTGCAt                                                                                                                                       >  2:887965/1‑140 (MQ=255) tttctttcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCAt                                                                                                                                       >  2:498429/1‑140 (MQ=255)     tttcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTgg                                                                                                                                   <  2:674888/140‑1 (MQ=255)     tttcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTgg                                                                                                                                   <  2:434270/140‑1 (MQ=255)       tcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTc                                                                                                                                 >  2:949093/1‑140 (MQ=255)       tcAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTc                                                                                                                                 >  1:777384/1‑140 (MQ=255)         aaTCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTcaa                                                                                                                               >  2:172189/1‑140 (MQ=255)              aTCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACaaaa                                                                                                                          >  2:732162/1‑140 (MQ=255)               tCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAAt                                                                                                                         <  1:88710/140‑1 (MQ=255)                 aGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCa                                                                                                                       <  2:321169/140‑1 (MQ=255)                        tttCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAaata                                                                                                                >  2:325051/1‑140 (MQ=255)                        tttCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAaata                                                                                                                <  2:15702/140‑1 (MQ=255)                                  tCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAAtaaattaaa                                                                                                      <  1:59598/140‑1 (MQ=255)                                        cacCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTtg                                                                                                <  1:445640/140‑1 (MQ=255)                                             tttGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCa                                                                                           <  1:105127/140‑1 (MQ=255)                                                   ggAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCa                                                                                     >  1:701357/1‑140 (MQ=255)                                                    gagaTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCaa                                                                                    <  1:887965/140‑1 (MQ=255)                                                     agaTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCaa                                                                                    <  2:197073/139‑1 (MQ=255)                                                     agaTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCaa                                                                                    >  1:197073/1‑139 (MQ=255)                                                       aTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCa                                                                                           <  1:360249/130‑1 (MQ=255)                                                       aTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCa                                                                                           >  2:360249/1‑130 (MQ=255)                                                         tttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgtt                                                                               >  2:333409/1‑140 (MQ=255)                                                          ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  1:990984/140‑1 (MQ=255)                                                          ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  2:1681/140‑1 (MQ=255)                                                          ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  2:388814/140‑1 (MQ=255)                                                          ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  1:605855/140‑1 (MQ=255)                                                          ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  2:428485/140‑1 (MQ=255)                                                              cAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGc                                                                          <  1:333409/140‑1 (MQ=255)                                                               aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                         <  2:777384/140‑1 (MQ=255)                                                               aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                         <  2:375051/140‑1 (MQ=255)                                                               aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                         <  1:498429/140‑1 (MQ=255)                                                               aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                         <  1:172189/140‑1 (MQ=255)                                                                agatCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              <  1:901944/131‑1 (MQ=255)                                                                agatCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                              >  2:901944/4‑134 (MQ=255)                                                                aGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCt                                                                        >  2:116095/1‑140 (MQ=255)                                                                    cATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTtata                                                                    <  1:732162/140‑1 (MQ=255)                                                                    cATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTtata                                                                    <  2:743492/140‑1 (MQ=255)                                                                           aTTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTa                                                             >  2:127753/1‑140 (MQ=255)                                                                           aTTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTa                                                             >  2:437541/1‑140 (MQ=255)                                                                            ttttttttCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTaa                                                            <  1:982885/140‑1 (MQ=255)                                                                                                     tctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACcaca                                          >  2:688993/1‑133 (MQ=255)                                                                                                     tctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACcaca                                          <  1:688993/133‑1 (MQ=255)                                                                                                      ctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGtgatga                                  <  1:949093/140‑1 (MQ=255)                                                                                                      ctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTCCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGtgatga                                  <  2:891293/140‑1 (MQ=255)                                                                                                       tctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTgatgat                                 >  1:16820/1‑140 (MQ=255)                                                                                                         tAAAAGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGatat                               >  1:424301/1‑140 (MQ=255)                                                                                                            aaGTGTTGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATtgt                            <  1:123669/140‑1 (MQ=255)                                                                                                                 ttGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAg                       >  2:542184/1‑140 (MQ=255)                                                                                                                 ttGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAg                       >  2:819900/1‑140 (MQ=255)                                                                                                                 ttGATGCAAGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAg                       >  1:634726/1‑140 (MQ=255)                                                                                                                        aaGTGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGa                <  1:542184/140‑1 (MQ=255)                                                                                                                           tGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGa                >  1:998763/1‑137 (MQ=255)                                                                                                                           tGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGa                <  2:998763/137‑1 (MQ=255)                                                                                                                           tGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc             <  2:634726/140‑1 (MQ=255)                                                                                                                           tGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc             <  2:137227/140‑1 (MQ=255)                                                                                                                           tGGTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc             <  1:819900/140‑1 (MQ=255)                                                                                                                             gTAACGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCg           <  2:605390/140‑1 (MQ=255)                                                                                                                                aCGGCGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGt        <  2:424301/140‑1 (MQ=255)                                                                                                                                    cGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTa                    >  2:847666/1‑124 (MQ=255)                                                                                                                                    cGATTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTa                    <  1:847666/124‑1 (MQ=255)                                                                                                                                      aTTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAt  >  2:425143/1‑140 (MQ=255)                                                                                                                                      aTTGCATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAt  >  2:752983/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                        TTTCTTTCAATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAT  >  NC_000913/2995933‑2996205

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑