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%	194.6 / NA	50	pseudogene (203/1241 nt)	yjhR	helicase YjhR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/25);  total (25/25)

CTCTCACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524676‑4524941                                                                                                                                       |                                                                                                                                    ctctCACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGgaa                                                                                                                                   >  2:279241/1‑137 (MQ=255)           cAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGAtttt                                                                                                                       >  2:10341/1‑139 (MQ=255)              tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                    >  1:181596/1‑139 (MQ=255)                  aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGc                                                                                                                 >  2:467383/1‑138 (MQ=255)                  aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  1:207891/139‑1 (MQ=255)                  aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  1:423277/139‑1 (MQ=255)                    cccAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                              >  2:454321/1‑139 (MQ=255)                              aGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTa                                                                                                    >  2:365629/1‑139 (MQ=255)                               gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  1:10341/139‑1 (MQ=255)                               gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  1:467383/139‑1 (MQ=255)                               gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  2:568156/139‑1 (MQ=255)                                    gAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              <  2:617953/139‑1 (MQ=255)                                         tATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATgg                                                                                         <  1:511831/139‑1 (MQ=255)                                               tATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAgg                                                                                   >  2:156645/1‑139 (MQ=255)                                                         gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                >  1:450668/1‑100 (MQ=255)                                                         gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  2:450668/100‑1 (MQ=255)                                                         gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGcc                                                                          >  1:581195/1‑138 (MQ=255)                                                         gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGcc                                                                          >  1:359306/1‑138 (MQ=255)                                                                              tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGa                                                                                                          >  1:539771/1‑85 (MQ=255)                                                                              tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGa                                                                                                          <  2:539771/85‑1 (MQ=255)                                                                              tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  2:491166/1‑139 (MQ=255)                                                                                    actGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  1:319316/1‑133 (MQ=255)                                                                                    actGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    <  2:319316/133‑1 (MQ=255)                                                                                    actGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCtt                                              >  1:594818/1‑139 (MQ=255)                                                                                        tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                           <  1:628969/74‑1 (MQ=255)                                                                                        tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                           >  2:628969/1‑74 (MQ=255)                                                                                             cACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCtt                                              <  1:240881/130‑1 (MQ=255)                                                                                             cACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCtt                                              >  2:240881/1‑130 (MQ=255)                                                                                              aCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        >  2:462060/1‑135 (MQ=255)                                                                                              aCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        <  1:462060/135‑1 (MQ=255)                                                                                              aCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGa                                      <  2:594818/137‑1 (MQ=255)                                                                                               cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGaaa                                    >  2:422346/1‑138 (MQ=255)                                                                                                tttGCTATCACGGTAAGTTGCAGCCTACAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        >  1:567669/1‑133 (MQ=255)                                                                                                tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGTAATGGGATATTTAc                                                                                                   <  1:594388/74‑1 (MQ=255)                                                                                                tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   >  2:594388/1‑74 (MQ=255)                                                                                                tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                        <  2:567669/133‑1 (MQ=255)                                                                                                tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAAc                                   >  1:480786/1‑138 (MQ=255)                                                                                                  tGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACaa                                 <  1:454382/138‑1 (MQ=255)                                                                                                          cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                              <  2:302935/53‑1 (MQ=255)                                                                                                          cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                              >  1:302935/1‑53 (MQ=255)                                                                                                          cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCAt                        >  1:563160/1‑139 (MQ=255)                                                                                                            gTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATgg                      >  1:76018/1‑139 (MQ=255)                                                                                                             tAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGc                     <  2:76018/139‑1 (MQ=255)                                                                                                                        cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt          <  2:181866/139‑1 (MQ=255)                                                                                                                        cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt          <  1:491166/139‑1 (MQ=255)                                                                                                                           aaaGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        <  2:181596/138‑1 (MQ=255)                                                                                                                             agagGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGga     <  1:422346/139‑1 (MQ=255)                                                                                                                             agagGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGga     <  1:156645/139‑1 (MQ=255)                                                                                                                                 ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        >  2:317943/1‑132 (MQ=255)                                                                                                                                 ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        <  1:317943/132‑1 (MQ=255)                                                                                                                                 ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGgatga  >  2:214616/1‑138 (MQ=255)                                                                                                                                       |                                                                                                                                    CTCTCACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524676‑4524941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑