Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,220,971	G→A	pseudogene (1371/2648 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	1,220,971	0	G	A	100.0%	194.5 / NA	57	pseudogene (1371/2648 nt)	ycgH	putative transporter component, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (32/25);  total (32/25)

ATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAATCTCC  >  NC_000913/1220835‑1221102                                                                                                                                            |                                                                                                                                    aTTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCt                                                                                                                                  <  1:100178/140‑1 (MQ=255)       aCAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGAc                                                                                                                            >  1:823320/1‑140 (MQ=255)           tattatCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGAc                                                                                                                        >  1:465895/1‑140 (MQ=255)            attatCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACt                                                                                                                       <  1:749079/140‑1 (MQ=255)            attatCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACt                                                                                                                       <  1:662084/140‑1 (MQ=255)                   aTCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                <  2:465895/140‑1 (MQ=255)                   aTCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                <  2:252139/140‑1 (MQ=255)                   aTCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                <  1:484913/140‑1 (MQ=255)                   aTCTTTCGTATGATGATCGTCACACATTTACCCAACGAATAACATTAATCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                <  2:225344/140‑1 (MQ=255)                     cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTGATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                <  2:356169/138‑1 (MQ=255)                     cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTGATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTAttgtt                                                                                                                >  1:356169/1‑138 (MQ=255)                     cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGa                                                                                                              >  1:117060/1‑140 (MQ=255)                     cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGa                                                                                                              >  1:129031/1‑140 (MQ=255)                       ttCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGAGATGATAGATCAGCTACGGACAGACTTATTGTTGAgg                                                                                                            >  1:225344/1‑140 (MQ=255)                         cGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGt                                                                                                          >  1:564347/1‑140 (MQ=255)                         cGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGt                                                                                                          >  2:544790/1‑140 (MQ=255)                                  atgGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCg                                                                                                 <  2:129031/140‑1 (MQ=255)                                  atgGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCg                                                                                                 <  1:80387/140‑1 (MQ=255)                                  atgGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCg                                                                                                 >  2:80387/1‑140 (MQ=255)                                     gTCAAACATTTACCTAATGAAAGGCATTTACCGTAGAAGTTAATAA‑‑‑TGTTGGTAATAATGGTGAGCTTAATATCCGCACCGTATTAGGAGAGAATAAATAAGCTATTGACAGAGTTATTATTGAGGGAAAATCTTCggtt                                                                                              >  2:394100/1‑138 (MQ=255)                                      tCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGtt                                                                                             <  1:646788/140‑1 (MQ=255)                                        aaaCATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCa                                                                                           >  2:794962/1‑140 (MQ=255)                                         aaCATTTACCCAAGGCAAAACAGTAGCCGAAAAAGGTAATTATGCTGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGtt                                                                                             <  1:384990/140‑1 (MQ=255)                                               tACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCg                                                                                    >  1:58151/1‑140 (MQ=255)                                                aCCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGt                                                                                   >  2:439350/1‑140 (MQ=255)                                                aCCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGt                                                                                   >  2:639753/1‑140 (MQ=255)                                                      ggAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTAtgt                                                                             >  1:42446/1‑140 (MQ=255)                                                                        aaaGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAg                                                           >  1:461395/1‑140 (MQ=255)                                                                              aaTTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAgcggcgc                                                     >  1:408581/1‑140 (MQ=255)                                                                                 tA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAgcggcgcggc                                                  <  1:274730/140‑1 (MQ=255)                                                                                        tCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACg                                              <  2:461395/140‑1 (MQ=255)                                                                                        tCGGTAATAATGGTCAGCTTAACATCCGCCCCGTATTTGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACg                                              <  1:394100/140‑1 (MQ=255)                                                                                         cGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAgcggcgcggc                                                  >  1:802790/1‑135 (MQ=255)                                                                                         cGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAgcggcgcggc                                                  <  2:802790/135‑1 (MQ=255)                                                                                                  tGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGTGGCCACGCTAAACGGGa                                    <  2:117060/140‑1 (MQ=255)                                                                                                  tGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGa                                    >  1:811852/1‑140 (MQ=255)                                                                                                  tGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGa                                    <  1:468486/140‑1 (MQ=255)                                                                                                     tCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCg                                 >  2:781558/1‑140 (MQ=255)                                                                                                      cAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGa                                <  1:668713/140‑1 (MQ=255)                                                                                                      cAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGa                                <  2:564347/140‑1 (MQ=255)                                                                                                        gCTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAAc                              <  2:811852/140‑1 (MQ=255)                                                                                                         cTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGTGGCGCGCCCACGCCAAACGGGATCGAACt                             >  1:284547/1‑140 (MQ=255)                                                                                                         cTTAATATCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACt                             <  2:823320/140‑1 (MQ=255)                                                                                                             atatCCGCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTTAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATa                         <  1:794962/140‑1 (MQ=255)                                                                                                                tCCGCACCGTATTAGGTCATGAAAAATCAGCCACGGACATACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACt                      <  2:240399/140‑1 (MQ=255)                                                                                                                   gCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACtgtg                   >  1:178012/1‑140 (MQ=255)                                                                                                                   gCACCGTATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACtgtg                   >  1:613677/1‑140 (MQ=255)                                                                                                                         tATTAGGTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGc             >  2:548572/1‑140 (MQ=255)                                                                                                                              ggTGATGATAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGa        <  1:544790/140‑1 (MQ=255)                                                                                                                                 gatgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtc     >  1:630084/1‑140 (MQ=255)                                                                                                                                 gatgatAAATCAGCTACAGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtc     >  1:494643/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCATCTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtctc   >  2:462544/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAAGGGGATCGGACTAATGACTGTGGATGGGGATGAAtctc   >  1:213648/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtctc   >  1:119058/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtctc   >  2:595779/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtctc   >  1:806023/1‑140 (MQ=255)                                                                                                                                   tgatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAAtctc   >  1:540787/1‑140 (MQ=255)                                                                                                                                    gatAAATCAGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAATCTcc  >  1:164812/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                    ATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTA‑‑‑TGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGAGGGTAATACTTCGGGTTCAACTACCGTCTATGTGAAAAATGCTGGAGGAAGCGGCGCGGCCACGCTAAACGGGATCGAACTCATAACTGTGAATGGCGATGAATCTCC  >  NC_000913/1220835‑1221102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑