Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,220,454	C→A	pseudogene (854/2648 nt)	ycgH →	putative transporter component, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,220,454	0	C	A	100.0%	220.7 / NA	63	pseudogene (854/2648 nt)	ycgH	putative transporter component, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (34/29);  total (34/29)

AATGGGAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGTTGAACT  >  NC_000913/1220318‑1220589                                                                                                                                         |                                                                                                                                        aaTGGGAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACAt                                                                                                                                      <  2:209307/140‑1 (MQ=255)   tGGGAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTg                                                                                                                                    >  1:727383/1‑140 (MQ=255)   tGGGAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTg                                                                                                                                    <  2:154040/140‑1 (MQ=255)     ggAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCa                                                                                                                                  >  2:192329/1‑140 (MQ=255)      gAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCaa                                                                                                                                 <  1:669594/140‑1 (MQ=255)       aaaaaaGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCaaa                                                                                                                                >  1:94069/1‑140 (MQ=255)           aaGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAata                                                                                                                            <  2:94615/140‑1 (MQ=255)             gCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAAtata                                                                                                                          <  2:721822/140‑1 (MQ=255)              cATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATAc                                                                                                                         >  1:634591/1‑140 (MQ=255)               atatatTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACa                                                                                                                        <  1:709910/140‑1 (MQ=255)                tatatTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACaa                                                                                                                       <  2:653939/140‑1 (MQ=255)                tatatTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACaa                                                                                                                       <  2:228704/140‑1 (MQ=255)                     tAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAAtggtg                                                                                                                  <  2:727383/140‑1 (MQ=255)                             aTTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTa                                                                                                          >  1:1724/1‑140 (MQ=255)                             aTTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTa                                                                                                          >  2:641731/1‑140 (MQ=255)                                 tgtgGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTAtttt                                                                                                      >  2:422892/1‑140 (MQ=255)                                 tgtgGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTAtttt                                                                                                      >  2:55987/1‑140 (MQ=255)                                          tGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATg                                                                                             >  1:100507/1‑140 (MQ=255)                                           gAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGt                                                                                            <  2:249785/140‑1 (MQ=255)                                                  tgGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACcgcg                                                                                     <  1:641731/140‑1 (MQ=255)                                                  tgGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACcgcg                                                                                     >  2:436445/1‑140 (MQ=255)                                                  tgGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACcgcg                                                                                     >  2:258857/1‑140 (MQ=255)                                                   ggCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCgg                                                                                    >  1:407449/1‑140 (MQ=255)                                                      tGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTAt                                                                                 <  1:195177/140‑1 (MQ=255)                                                           gAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCaaaa                                                                            <  2:94069/140‑1 (MQ=255)                                                            aaGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAAc                                                                           >  2:616132/1‑140 (MQ=255)                                                              gTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACaa                                                                         >  1:339697/1‑140 (MQ=255)                                                              gTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACaa                                                                         >  2:186959/1‑140 (MQ=255)                                                               ttATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCaaaa                                                                            <  2:515633/136‑1 (MQ=255)                                                               ttATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCaaaa                                                                            >  1:515633/1‑136 (MQ=255)                                                                tATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGa                                                                       <  2:328591/140‑1 (MQ=255)                                                                 aTGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGAt                                                                      <  1:192329/140‑1 (MQ=255)                                                                  tGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATa                                                                     <  1:611653/140‑1 (MQ=255)                                                                   gCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAGCAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATaa                                                                    <  1:724974/140‑1 (MQ=255)                                                                    cAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATaaa                                                                   <  1:707276/140‑1 (MQ=255)                                                                      gTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAgg                                                                 >  2:682375/1‑140 (MQ=255)                                                                         gCTATTCAACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAat                                                              <  2:339722/140‑1 (MQ=255)                                                                               cGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAAt                                                        >  1:488495/1‑140 (MQ=255)                                                                                 aCAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTg                                                      <  2:385848/140‑1 (MQ=255)                                                                                     ggTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGc                                                  >  2:584004/1‑140 (MQ=255)                                                                                            ttGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAat                                           <  2:30129/140‑1 (MQ=255)                                                                                              gATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAatat                                         >  1:544049/1‑140 (MQ=255)                                                                                               atatAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATc                                        >  1:161071/1‑140 (MQ=255)                                                                                               atatAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATc                                        >  1:660077/1‑140 (MQ=255)                                                                                                tataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCg                                       >  1:385087/1‑140 (MQ=255)                                                                                                tataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCg                                       >  1:293575/1‑140 (MQ=255)                                                                                                tataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCg                                       >  1:147998/1‑140 (MQ=255)                                                                                                 ataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGa                                      >  1:404309/1‑140 (MQ=255)                                                                                                               tATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCaaaa                        <  1:611749/140‑1 (MQ=255)                                                                                                               tATTACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCaaaa                        <  1:682375/140‑1 (MQ=255)                                                                                                                  tACAACAACAGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAg                     <  1:133217/140‑1 (MQ=255)                                                                                                                    caacaacaGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCa                   <  2:473636/140‑1 (MQ=255)                                                                                                                      acaacaGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGTCAAAATAGCACt                 <  2:334894/140‑1 (MQ=255)                                                                                                                      acaacaGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACt                 >  1:605339/1‑140 (MQ=255)                                                                                                                         acaGGCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTAtt              >  2:214718/1‑140 (MQ=255)                                                                                                                            ggCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAg           >  2:166019/1‑140 (MQ=255)                                                                                                                            ggCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAg           >  1:460860/1‑140 (MQ=255)                                                                                                                            ggCACTAAAGCCCACAGTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAg           >  2:459728/1‑140 (MQ=255)                                                                                                                             gCACTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAgt          >  2:268147/1‑140 (MQ=255)                                                                                                                               aCTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAg                     <  2:555744/127‑1 (MQ=255)                                                                                                                               aCTAAAGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAg                     >  1:555744/1‑127 (MQ=255)                                                                                                                                  aaaGCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGTTGa     <  2:660077/140‑1 (MQ=255)                                                                                                                                     gCCCACATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGTTGAACt  >  2:53229/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                        AATGGGAAAAAAGCATATATTAATTTAGATTATGTGGCACTTGAAACTGTGGCTGATGGAAGTTATGCAGTTGCTATTCGACAAGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGTTGAACT  >  NC_000913/1220318‑1220589

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑