Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,524,810	A→G	pseudogene (203/1241 nt)	yjhR →	helicase YjhR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,524,810	0	A	G	100.0%	271.0 / NA	68	pseudogene (203/1241 nt)	yjhR	helicase YjhR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (39/29);  total (39/29)

TCACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524679‑4524941                                                                                                                                    |                                                                                                                                    tcACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGa                                                                                                                              >  2:584789/1‑139 (MQ=255)   aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCCCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACg                                                                                                                            <  1:224112/139‑1 (MQ=255)   aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGAc                                                                                                                             >  2:493040/1‑138 (MQ=255)           tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                    >  2:19600/1‑139 (MQ=255)           tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                    >  1:575144/1‑139 (MQ=255)               aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGc                                                                                                                 >  2:750308/1‑138 (MQ=255)               aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGc                                                                                                                 >  1:546444/1‑138 (MQ=255)               aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  1:245697/139‑1 (MQ=255)                 cccAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  2:93098/137‑1 (MQ=255)                 cccAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                >  1:93098/1‑137 (MQ=255)                  ccAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATg                                                                                                             >  2:706804/1‑139 (MQ=255)                     aGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGa                                                                                                          >  2:19256/1‑139 (MQ=255)                          gAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATAtt                                                                                                      <  1:330591/138‑1 (MQ=255)                           aGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTa                                                                                                    >  1:61751/1‑139 (MQ=255)                            gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  1:19600/139‑1 (MQ=255)                               cgGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACata                                                                                                >  1:359270/1‑139 (MQ=255)                                   aTGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGa                                                                                            <  2:359270/139‑1 (MQ=255)                                   aTGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGa                                                                                            <  1:323404/139‑1 (MQ=255)                                            tATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAgg                                                                                   >  1:343517/1‑139 (MQ=255)                                              tGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCa                                                                                 <  2:629920/139‑1 (MQ=255)                                              tGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCa                                                                                 >  1:116296/1‑139 (MQ=255)                                                aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCAt                                                                                >  2:200708/1‑138 (MQ=255)                                                aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCAt                                                                                >  1:241587/1‑138 (MQ=255)                                                  cATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGaa                                                                             <  2:58857/139‑1 (MQ=255)                                                    tcgtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGc                                                                           >  2:52234/1‑139 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGTCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGaa                                                                             <  1:65252/135‑1 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATAtt                                                                                                      <  1:649126/110‑1 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATAtt                                                                                                      >  2:649126/1‑110 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGaa                                                                             >  2:65252/1‑135 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGcc                                                                          >  1:218012/1‑138 (MQ=255)                                                      gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGcc                                                                          >  1:689245/1‑138 (MQ=255)                                                                 aaTAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                              <  1:584789/139‑1 (MQ=255)                                                                       atcatcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCaa                                                                                                               <  1:583397/84‑1 (MQ=255)                                                                       atcatcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCaa                                                                                                               >  2:583397/1‑84 (MQ=255)                                                                           tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              >  2:90960/1‑97 (MQ=255)                                                                           tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              <  1:90960/97‑1 (MQ=255)                                                                           tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATTAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  1:224147/1‑139 (MQ=255)                                                                                 actGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCtt                                              >  2:260310/1‑139 (MQ=255)                                                                                     tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                           <  1:283115/74‑1 (MQ=255)                                                                                     tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                           >  2:283115/1‑74 (MQ=255)                                                                                       aCTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        <  2:730342/139‑1 (MQ=255)                                                                                            cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggag                                                                  <  2:173052/108‑1 (MQ=255)                                                                                            cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggag                                                                  >  1:173052/1‑108 (MQ=255)                                                                                            cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGaaa                                    >  2:730950/1‑138 (MQ=255)                                                                                            cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGaaa                                    >  1:343033/1‑138 (MQ=255)                                                                                             tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAAc                                   >  1:333303/1‑138 (MQ=255)                                                                                                     cACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATagcag                           >  1:623671/1‑138 (MQ=255)                                                                                                       cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAAt                                                                      <  2:132129/93‑1 (MQ=255)                                                                                                       cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAAt                                                                      >  1:132129/1‑93 (MQ=255)                                                                                                       cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        >  1:279363/1‑123 (MQ=255)                                                                                                       cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        <  2:279363/123‑1 (MQ=255)                                                                                                       cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCAt                        >  2:610361/1‑139 (MQ=255)                                                                                                            aGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAACCAATAGCAGCATGGCtg                   <  2:689245/139‑1 (MQ=255)                                                                                                            aGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtg                   >  1:612986/1‑139 (MQ=255)                                                                                                              ttGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  1:128890/44‑1 (MQ=255)                                                                                                              ttGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                >  2:128890/1‑44 (MQ=255)                                                                                                                gCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtg                <  2:530771/138‑1 (MQ=255)                                                                                                                 cAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtgg               <  1:730950/138‑1 (MQ=255)                                                                                                                 cAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGc              <  1:269933/139‑1 (MQ=255)                                                                                                                    ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATg                                                                               >  1:346082/1‑71 (MQ=255)                                                                                                                    ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATg                                                                               <  2:346082/71‑1 (MQ=255)                                                                                                                    ccTAAAAGAGAGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  2:581209/1‑98 (MQ=255)                                                                                                                    ccTAAAAGAGAGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    <  1:581209/98‑1 (MQ=255)                                                                                                                     cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt          <  2:575144/139‑1 (MQ=255)                                                                                                                        aaaGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        <  1:260310/138‑1 (MQ=255)                                                                                                                         aaGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAgg      <  2:116296/139‑1 (MQ=255)                                                                                                                              ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGgatga  >  1:234992/1‑138 (MQ=255)                                                                                                                              ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGgatga  >  2:732465/1‑138 (MQ=255)                                                                                                                                    |                                                                                                                                    TCACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524679‑4524941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑