Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,059,555	C→A	pseudogene (57/231 nt)	yqfE ←	conserved protein YqfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,059,555	0	C	A	100.0%	187.5 / NA	54	pseudogene (57/231 nt)	yqfE	conserved protein YqfE
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (23/31);  total (23/31)

AAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGCAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCTTCGGT  >  NC_000913/3059421‑3059684                                                                                                                                       |                                                                                                                                  aaaTATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATaa                                                                                                                              >  1:723273/1‑140 (MQ=255) aaaTATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATaa                                                                                                                              >  1:223939/1‑140 (MQ=255)     atCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAA‑CCCCTGTTTACAGGCAAATTGAGGAAAAAaagcca                                                                                                                         >  1:463006/1‑140 (MQ=255)        gcgcAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAacgccacg                                                                                                                       <  1:565392/140‑1 (MQ=255)        gcgcAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAacgccacg                                                                                                                       <  1:51728/140‑1 (MQ=255)        gcgcAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAacgccacg                                                                                                                       <  2:564253/140‑1 (MQ=255)         cgcAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAacgccacgc                                                                                                                      >  1:1140356/1‑140 (MQ=255)           cAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAAcgccacgcca                                                                                                                    <  2:280799/140‑1 (MQ=255)           cAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAAcgccacgcca                                                                                                                    <  1:508224/140‑1 (MQ=255)           cAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAAcgccacgcca                                                                                                                    <  1:243890/140‑1 (MQ=255)                gcaggcaTCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCGCCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCaa                                                                                                               <  1:55320/140‑1 (MQ=255)                gcaggcaTCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAATGCCACGCCATTCaa                                                                                                               <  1:520197/140‑1 (MQ=255)                gcaggcaTCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCaa                                                                                                               <  2:34356/140‑1 (MQ=255)                gcaggcaTCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCaa                                                                                                               <  1:617598/140‑1 (MQ=255)                                 ccccGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGaa                                                                                              >  2:334922/1‑140 (MQ=255)                                      cAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGc                                                                                         >  2:428365/1‑140 (MQ=255)                                          tAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAg                                                                                     <  2:884824/140‑1 (MQ=255)                                                          cTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAgcgc                                                                     >  1:473905/1‑140 (MQ=255)                                                                  gCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCt                                                             >  2:885144/1‑140 (MQ=255)                                                                  gCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCt                                                             >  2:403211/1‑140 (MQ=255)                                                                   ccGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTg                                                            >  2:284247/1‑140 (MQ=255)                                                                   ccGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTg                                                            <  1:885144/140‑1 (MQ=255)                                                                   ccGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTg                                                            <  2:473905/140‑1 (MQ=255)                                                                   ccGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTg                                                            >  2:310799/1‑140 (MQ=255)                                                                   ccGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTg                                                            <  1:334922/140‑1 (MQ=255)                                                                       tCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCt                                                        >  1:943195/1‑140 (MQ=255)                                                                       tCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCt                                                        >  1:1109313/1‑140 (MQ=255)                                                                       tCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCt                                                        >  1:673182/1‑140 (MQ=255)                                                                       tCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCt                                                        >  2:989264/1‑140 (MQ=255)                                                                           cGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTa                                                    >  1:53269/1‑140 (MQ=255)                                                                               gCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCt                                                <  2:427767/140‑1 (MQ=255)                                                                                cAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTg                                               <  2:984593/140‑1 (MQ=255)                                                                                        cgcACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTa                                       >  1:993306/1‑140 (MQ=255)                                                                                           aCCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAAcc                                    <  1:284247/140‑1 (MQ=255)                                                                                           aCCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAAcc                                    <  1:310799/140‑1 (MQ=255)                                                                                           aCCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAAcc                                    <  2:1117149/140‑1 (MQ=255)                                                                                             cAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCAc                                  <  2:12461/140‑1 (MQ=255)                                                                                             cAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCAc                                  <  2:993306/140‑1 (MQ=255)                                                                                             cAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCAc                                  <  2:1109313/140‑1 (MQ=255)                                                                                                ttCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGa                               <  2:1140356/140‑1 (MQ=255)                                                                                                  cACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATa                             <  2:475809/140‑1 (MQ=255)                                                                                                       ttCGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAAt                        >  2:433807/1‑140 (MQ=255)                                                                                                         cGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGt                      >  1:829711/1‑140 (MQ=255)                                                                                                         cGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGt                      >  1:585369/1‑140 (MQ=255)                                                                                                         cGCAAGCCCCTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGt                      >  2:783875/1‑140 (MQ=255)                                                                                                                 ccTGTTTACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACccgcc              >  1:650069/1‑140 (MQ=255)                                                                                                                   tGTTTAGAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAGCCAGGGCGCGAACCCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCAGGGATCCAAATGTTACCCGCCGa            <  2:723273/140‑1 (MQ=255)                                                                                                                    gTTTACAGGCAAATTGAGGAAATACCGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGAc           <  1:1131884/140‑1 (MQ=255)                                                                                                                      ttACAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACgg         <  1:428365/140‑1 (MQ=255)                                                                                                                        aCAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCt       <  1:695886/140‑1 (MQ=255)                                                                                                                        aCAGGCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCt       <  2:463006/140‑1 (MQ=255)                                                                                                                            gCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGTTTTTAACCACGGATACAAATGTTACCCGCCGACGGCTTCgg   <  2:223939/140‑1 (MQ=255)                                                                                                                            gCAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCTTCgg   <  1:433807/140‑1 (MQ=255)                                                                                                                             cAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCTTCGGt  >  2:1158398/1‑140 (MQ=255)                                                                                                                             cAAATTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTAAACCACGGATACAAATGTTACCCGCCGACGGCTTCGGt  <  2:53269/140‑1 (MQ=255)                                                                                                                               aaTTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGa            >  1:1073617/1‑128 (MQ=255)                                                                                                                               aaTTGAGGAAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGa            <  2:1073617/128‑1 (MQ=255)                                                                                                                                       |                                                                                                                                  AAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTTCACCGTTCGCAAGCCCCTGTTTACAGGCAAATTGAGGCAATAACGCCACGCCATTCAACACAACCAGGGCGCGAACTCGCTGAGCGAAATGCATTAGCGCAAATCCCTGATCTTTTAAGCTGCGCTTTTAACCACGGATACAAATGTTACCCGCCGACGGCTTCGGT  >  NC_000913/3059421‑3059684

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑