Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,996,077	T→C	pseudogene (284/399 nt)	ygeO ←	putative uncharacterized protein YgeO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,996,077	0	T	C	100.0%	207.0 / NA	57	pseudogene (284/399 nt)	ygeO	putative uncharacterized protein YgeO
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/33);  total (24/33)

AATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGC  >  NC_000913/2995941‑2996210                                                                                                                                         |                                                                                                                                      aaTCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCcaa                                                                                                                                    >  1:495415/1‑140 (MQ=255) aaTCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCcaa                                                                                                                                    >  1:87925/1‑140 (MQ=255)      aTCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACaaaa                                                                                                                               >  2:345346/1‑140 (MQ=255)      aTCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACaaaa                                                                                                                               >  2:345347/1‑140 (MQ=255)            aaTTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGa                                                                                                                         <  1:37140/140‑1 (MQ=255)                tttCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAaata                                                                                                                     <  2:692196/140‑1 (MQ=255)                             caacaCCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCg                                                                                                        <  2:23742/140‑1 (MQ=255)                               acacCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGtt                                                                                                      <  2:417600/140‑1 (MQ=255)                                cacCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTtg                                                                                                     <  1:567637/140‑1 (MQ=255)                                     tttGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCa                                                                                                >  2:883994/1‑140 (MQ=255)                                        gCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGtt                                                                                                      <  2:191564/131‑1 (MQ=255)                                        gCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGtt                                                                                                      >  1:191564/1‑131 (MQ=255)                                           ggAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCa                                                                                          >  1:916576/1‑140 (MQ=255)                                            gagaTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCaa                                                                                         <  2:87925/140‑1 (MQ=255)                                            gagaTTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCaa                                                                                         >  2:598125/1‑140 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  2:716206/140‑1 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  1:598125/140‑1 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  1:495079/140‑1 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  1:277874/140‑1 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  1:262379/140‑1 (MQ=255)                                                  ttATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTAGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttg                                                                                   <  2:495859/140‑1 (MQ=255)                                                   tATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttgt                                                                                  <  1:345347/140‑1 (MQ=255)                                                   tATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGgttgt                                                                                  <  1:345346/140‑1 (MQ=255)                                                      cAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGc                                                                               <  2:495415/140‑1 (MQ=255)                                                       aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                              <  2:916576/140‑1 (MQ=255)                                                       aaGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGcc                                                                              <  1:289155/140‑1 (MQ=255)                                                          cTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTta                                                                           >  2:234848/1‑140 (MQ=255)                                                          cTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTta                                                                           >  2:266716/1‑140 (MQ=255)                                                                          ttCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGt                                                           >  1:275943/1‑140 (MQ=255)                                                                                    aTGTAATTCTCTCTGAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACca                                                 <  2:430660/140‑1 (MQ=255)                                                                                    aTGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACca                                                 <  2:275943/140‑1 (MQ=255)                                                                                     tGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACcac                                                <  2:184932/140‑1 (MQ=255)                                                                                      gtcaTTCTCTCTAAAAGTGTTGATGCAAGTAGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACcaca                                               <  2:583071/137‑1 (MQ=255)                                                                                        aaTTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACAtg                                             <  1:366475/140‑1 (MQ=255)                                                                                            ctctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGtgat                                         <  1:250059/140‑1 (MQ=255)                                                                                             tctctAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGtgatg                                        >  1:566846/1‑140 (MQ=255)                                                                                               tctAAAAGTGTTGATGCTTGTGGTAACGGCGATTGTATGTGTCCAACACAATCAGGAGATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCTTTATATAGGGTAATAACGTTGAAAAACCACATgtggtggt                                      >  2:8800/1‑138 (MQ=255)                                                                                                         ttGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAg                            >  1:93814/1‑140 (MQ=255)                                                                                                         ttGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAg                            >  2:748242/1‑140 (MQ=255)                                                                                                          tGATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGt                           <  2:808699/140‑1 (MQ=255)                                                                                                           gATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGtt                          >  2:813257/1‑140 (MQ=255)                                                                                                           gATGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGtt                          >  2:132404/1‑140 (MQ=255)                                                                                                             tGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTTAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTa                         <  1:169034/139‑1 (MQ=255)                                                                                                             tGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTTAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTa                         >  2:169034/1‑139 (MQ=255)                                                                                                             tGCAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAg                        <  1:234848/140‑1 (MQ=255)                                                                                                               cAAGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCg                      >  2:146074/1‑140 (MQ=255)                                                                                                                 aGTGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATTGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGAt                    >  2:619310/1‑140 (MQ=255)                                                                                                                   tGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc                  <  2:144177/140‑1 (MQ=255)                                                                                                                   tGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc                  <  1:748242/140‑1 (MQ=255)                                                                                                                   tGGTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGc                  <  1:121817/140‑1 (MQ=255)                                                                                                                     gTAACGGCGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCg                >  2:587080/1‑140 (MQ=255)                                                                                                                            cGATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGt         >  2:651856/1‑140 (MQ=255)                                                                                                                             gATTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTa        <  2:93814/140‑1 (MQ=255)                                                                                                                              aTTGTATGTGGCCAACAAAATCAGGCAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAt       >  2:551259/1‑140 (MQ=255)                                                                                                                              aTTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAt       >  2:707807/1‑140 (MQ=255)                                                                                                                              aTTGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGCTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTAt       >  2:377773/1‑140 (MQ=255)                                                                                                                                tGTATGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCg     <  1:266716/140‑1 (MQ=255)                                                                                                                                   aTGTGGCCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAACGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGc  <  1:212605/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                      AATCCATCAGAAATTTTTCTTTTAATCACAACACCATTTGCAGGAGATTTTATCAAGCTCATCTCTATTTTTTTTCGCATAAAATGTAATTCTCTCTAAAAGTGTTGATGCAAGTGGTAACGGCGATTGTATGTGGTCAACAAAATCAGGAAATAATAAATTAAATCGTTGCTGCATTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGC  >  NC_000913/2995941‑2996210

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: ‑