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%	212.6 / NA	53	pseudogene (203/1241 nt)	yjhR	helicase YjhR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/26);  total (27/26)

ACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGG  >  NZ_CP009273/4524681‑4524937                                                                                                                                  |                                                                                                                                aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGAc                                                                                                                         >  1:69300/1‑138 (MQ=255)         tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                >  2:553151/1‑139 (MQ=255)         tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                >  2:444002/1‑139 (MQ=255)           tGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCg                                                                                                              >  2:339512/1‑139 (MQ=255)             aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                            <  2:427719/139‑1 (MQ=255)                ccAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                          <  1:553151/138‑1 (MQ=255)                 cAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATgg                                                                                                        >  2:364168/1‑139 (MQ=255)                  aaGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                       <  2:273957/139‑1 (MQ=255)                  aaGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                       <  1:307388/139‑1 (MQ=255)                   aGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGa                                                                                                      <  2:356523/139‑1 (MQ=255)                   aGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGa                                                                                                      >  2:239679/1‑139 (MQ=255)                       cGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGatat                                                                                                   <  1:364168/138‑1 (MQ=255)                         aGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTa                                                                                                >  1:317414/1‑139 (MQ=255)                         aGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTa                                                                                                >  1:331917/1‑139 (MQ=255)                                          tATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAgg                                                                               >  1:528139/1‑139 (MQ=255)                                            tGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCa                                                                             >  1:214384/1‑139 (MQ=255)                                              aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATg                                                                           <  1:444002/139‑1 (MQ=255)                                                cATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCGCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATg                                                                           >  1:129694/1‑137 (MQ=255)                                                  tcgtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATAtt                                                                                                  >  1:105857/1‑112 (MQ=255)                                                  tcgtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATAtt                                                                                                  <  2:105857/112‑1 (MQ=255)                                                    gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCa                                                                             >  1:243602/1‑131 (MQ=255)                                                    gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCa                                                                             <  2:243602/131‑1 (MQ=255)                                                    gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGcc                                                                      >  1:140350/1‑138 (MQ=255)                                                     tcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCaa                                                                    <  1:555176/139‑1 (MQ=255)                                                               aaTAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                          <  2:99209/139‑1 (MQ=255)                                                                   aCATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                          >  2:299224/1‑103 (MQ=255)                                                                   aCATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                          <  1:299224/103‑1 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                          >  1:345377/1‑129 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                          <  2:345377/129‑1 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                >  2:291212/1‑139 (MQ=255)                                                                                ctGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCtt                                          <  1:291212/138‑1 (MQ=255)                                                                                   tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAg                                      <  2:214384/139‑1 (MQ=255)                                                                                   tAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAg                                      >  2:562632/1‑139 (MQ=255)                                                                                          cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGaaa                                >  2:29704/1‑138 (MQ=255)                                                                                           tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                >  1:409156/1‑57 (MQ=255)                                                                                           tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                <  2:409156/57‑1 (MQ=255)                                                                                           tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                >  1:277142/1‑57 (MQ=255)                                                                                           tttGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                <  2:277142/57‑1 (MQ=255)                                                                                                     cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCAt                    >  2:311123/1‑139 (MQ=255)                                                                                                               cAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtgg           <  2:28312/138‑1 (MQ=255)                                                                                                               cAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtgg           <  1:208373/138‑1 (MQ=255)                                                                                                                  ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                    >  1:87990/1‑110 (MQ=255)                                                                                                                  ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCt                                    <  2:87990/110‑1 (MQ=255)                                                                                                                  ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAAc                               <  1:18311/115‑1 (MQ=255)                                                                                                                  ccTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAAc                               >  2:18311/1‑115 (MQ=255)                                                                                                                   cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt      <  2:482041/139‑1 (MQ=255)                                                                                                                       aaGAGGGATGGGAAAAGGACGATTTTTCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAgg  <  1:365122/139‑1 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                >  1:69383/1‑86 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                <  2:69383/86‑1 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtg            <  1:469923/122‑1 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCtggtg            >  2:469923/1‑122 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt      >  2:366758/1‑128 (MQ=255)                                                                                                                              aTGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt      <  1:366758/128‑1 (MQ=255)                                                                                                                                  |                                                                                                                                ACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGG  >  NZ_CP009273/4524681‑4524937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑