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%	171.2 / NA	44	pseudogene (203/1241 nt)	yjhR	helicase YjhR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (23/21);  total (23/21)

ACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524681‑4524941                                                                                                                                  |                                                                                                                                    aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAgg                                                                                                                               <  2:436804/136‑1 (MQ=255) aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGAc                                                                                                                             >  1:157119/1‑138 (MQ=255) aCTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGAc                                                                                                                             >  1:361684/1‑138 (MQ=255)         tATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTccc                                                                                                                    >  2:193442/1‑139 (MQ=255)             aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGc                                                                                                                 >  1:212594/1‑138 (MQ=255)             aTCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGc                                                                                                                 >  2:441564/1‑138 (MQ=255)                  aaGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATggg                                                                                                           <  1:193442/139‑1 (MQ=255)                          gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  1:426224/139‑1 (MQ=255)                          gcgcGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTAc                                                                                                   <  1:11915/139‑1 (MQ=255)                               gAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              >  2:210257/1‑139 (MQ=255)                                          tATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAgg                                                                                   >  1:309366/1‑139 (MQ=255)                                              atcATCGTCGTTGTTTCAATAACATCATAGACTACTGTAACTCACTTTGCTATCACGGCAAGTTGCAGCCTAAAAGAGGGACGGGAAAAGGACGATTTTCCCCGCAATGGGCTATTTACATATACGTGGTAGAGGCAt                                                                                >  2:35049/3‑138 (MQ=255)                                              aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                              >  2:188108/1‑108 (MQ=255)                                              aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAAt                                                                                                              <  1:188108/108‑1 (MQ=255)                                              aGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCAt                                                                                >  1:43359/1‑138 (MQ=255)                                                cATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                >  2:279107/1‑104 (MQ=255)                                                cATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCa                                                                                                                <  1:279107/104‑1 (MQ=255)                                                    gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACata                                                                                                >  1:417854/1‑116 (MQ=255)                                                    gtcgCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACata                                                                                                <  2:417854/116‑1 (MQ=255)                                                       gCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCaaa                                                                       <  1:471516/138‑1 (MQ=255)                                                       gCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAAt                                                                      <  1:210257/139‑1 (MQ=255)                                                               aaTAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                              <  1:441564/139‑1 (MQ=255)                                                                     atcatcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCa                                                        >  1:255206/1‑139 (MQ=255)                                                                       catcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                              <  1:380605/131‑1 (MQ=255)                                                                       catcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagggag                                                              >  2:380605/1‑131 (MQ=255)                                                                        atcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATaa                                                     <  2:309366/139‑1 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagg                                                                 <  2:360615/126‑1 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATggagg                                                                 >  1:360615/1‑126 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  1:328465/1‑139 (MQ=255)                                                                         tcGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAAc                                                    >  1:205445/1‑139 (MQ=255)                                                                                        cACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGa                                      >  1:355884/1‑138 (MQ=255)                                                                                         aCTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGa                                      <  2:453180/137‑1 (MQ=255)                                                                                          cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATgg                                                                                                            >  2:37796/1‑66 (MQ=255)                                                                                          cTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATgg                                                                                                            <  1:37796/66‑1 (MQ=255)                                                                                             tGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              >  2:250093/1‑77 (MQ=255)                                                                                             tGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATAtt                                                                                              <  1:250093/77‑1 (MQ=255)                                                                                             tGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACaa                                 >  1:266587/1‑138 (MQ=255)                                                                                              gCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAAt                                <  2:328465/138‑1 (MQ=255)                                                                                                     cGGTAAGTTGCAGCCTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCAt                        >  2:188575/1‑139 (MQ=255)                                                                                                                   cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTTAAACAATAGCAGCATGGCTGGTGGCACAt          <  2:241996/139‑1 (MQ=255)                                                                                                                   cTAAAAGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACAt          <  2:157119/139‑1 (MQ=255)                                                                                                                      aaaGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        <  2:361684/138‑1 (MQ=255)                                                                                                                      aaaGAGGGATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATaa        <  2:404024/138‑1 (MQ=255)                                                                                                                            ggATGGGAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGgatga  >  1:453693/1‑138 (MQ=255)                                                                                                                                  |                                                                                                                                    ACTACCAGTATGATCCCAAGTTCGAGCGCGGAATGTATCTGTATGAGCATCGTCGCTGTTTCAATAACATCATCGACTACTGTAACTCACTTTGCTATCACGGTAAGTTGCAGCCTAAAAGAGGGATGGAAAAAGGACGATTTTCCCCGCAATGGGATATTTACATATTGATGGTAGAGGCATGAAGCCAAATGGAGGGAGCCGTCATAACCCTCTTGAAGCTGAAACAATAGCAGCATGGCTGGTGGCACATAAGGATGA  >  NZ_CP009273/4524681‑4524941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑