Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	453,912	A→G	E344G (GAA→GGA)	clpX →	ATP‑dependent protease ATP‑binding subunit ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	453,912	0	A	G	100.0%	202.8 / NA	54	E344G (GAA→GGA)	clpX	ATP‑dependent protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (24/30);  total (24/30)

GTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGAAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGATCTGCC  >  NZ_CP009273/453777‑454044                                                                                                                                        |                                                                                                                                     gTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAgg                                                                                                                                   >  2:361871/1‑139 (MQ=255) gTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAgg                                                                                                                                   >  2:33848/1‑139 (MQ=255) gTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAgg                                                                                                                                   >  1:287553/1‑139 (MQ=255)      aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGt                                                                                                                                <  2:130479/137‑1 (MQ=255)      aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGt                                                                                                                                <  1:822557/137‑1 (MQ=255)                         gtcTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGAc                                                                                                             >  1:393817/1‑137 (MQ=255)                              ccGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAgg                                                                                                         <  2:783264/136‑1 (MQ=255)                                 gTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTgg                                                                                                   <  2:393817/139‑1 (MQ=255)                                 gTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTg                                                                                                    >  1:577354/1‑138 (MQ=255)                                            gTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCt                                                                                        <  2:39924/139‑1 (MQ=255)                                                     aCTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCt                                                                                              >  1:329091/1‑124 (MQ=255)                                                     aCTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCt                                                                                              <  2:329091/124‑1 (MQ=255)                                                        gAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATg                                                                            >  2:72723/1‑139 (MQ=255)                                                         aGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATg                                                                            <  1:301583/138‑1 (MQ=255)                                                          gCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGgc                                                                          >  2:312980/1‑139 (MQ=255)                                                              agaagCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGcgcg                                                                       >  1:820335/1‑138 (MQ=255)                                                                   ctctGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAAc                                                                 >  1:212857/1‑139 (MQ=255)                                                                             gATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGt                                                       <  1:62618/139‑1 (MQ=255)                                                                                  tCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCt                                                  >  2:283225/1‑139 (MQ=255)                                                                                  tCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCt                                                  >  2:121565/1‑139 (MQ=255)                                                                                  tCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACAAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCt                                                  >  1:435185/1‑139 (MQ=255)                                                                                       gagCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGtt                                             <  2:212857/139‑1 (MQ=255)                                                                                        agCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCt                                                                                        <  1:5761/95‑1 (MQ=255)                                                                                        agCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCt                                                                                        >  2:5761/1‑95 (MQ=255)                                                                                        agCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTc                                            >  1:502015/1‑139 (MQ=255)                                                                                          ccGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAAcc                                                                <  1:672203/117‑1 (MQ=255)                                                                                          ccGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAAcc                                                                >  2:672203/1‑117 (MQ=255)                                                                                           cGAAAAACGCCCTGACCAAGCAGTGTCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCAt                                         >  1:39996/1‑139 (MQ=255)                                                                                                   gCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAg                                 <  1:783602/139‑1 (MQ=255)                                                                                                      cTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACAAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCg                              <  2:435185/139‑1 (MQ=255)                                                                                                       tGACCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCg                              >  1:323260/1‑138 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTg                                                                                                               <  2:411750/55‑1 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTg                                                                                                               >  1:411750/1‑55 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGtt                                             >  1:693460/1‑121 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGtt                                             <  2:693460/121‑1 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCa                            <  1:29787/138‑1 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCa                            <  1:33848/138‑1 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCa                            <  1:651961/138‑1 (MQ=255)                                                                                                         aCCAAGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCAc                           >  2:45852/1‑139 (MQ=255)                                                                                                             aGCAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCt                       <  1:741672/139‑1 (MQ=255)                                                                                                               cAGTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCg                     <  1:361871/139‑1 (MQ=255)                                                                                                                 gTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGAt                   <  1:402268/139‑1 (MQ=255)                                                                                                                 gTATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGAt                   <  1:45852/139‑1 (MQ=255)                                                                                                                  tATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTcctgt                  <  1:846090/139‑5 (MQ=255)                                                                                                                  tATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATa                  >  1:277000/1‑139 (MQ=255)                                                                                                                  tATCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATa                  <  2:431272/139‑1 (MQ=255)                                                                                                                    tCAGGCGCTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATAc                 <  2:323260/138‑1 (MQ=255)                                                                                                                        gcgcTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGt            <  2:277000/139‑1 (MQ=255)                                                                                                                        gcgcTGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGt            <  2:39996/139‑1 (MQ=255)                                                                                                                            tGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGa        >  2:385856/1‑139 (MQ=255)                                                                                                                            tGTTTAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGa        >  2:331648/1‑139 (MQ=255)                                                                                                                              tttAATCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGAt       <  1:121565/138‑1 (MQ=255)                                                                                                                                 aaTCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGATCTg    <  2:21526/138‑1 (MQ=255)                                                                                                                                  aTCTGGGAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGATCTGcc  <  1:312980/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                     GTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATTCAGATCCTCAAAGAGCCGAAAAACGCCCTGACCAAGCAGTATCAGGCGCTGTTTAATCTGGAAGGCGTGGATCTGGAATTCCGTGACGAGGCGCTGGATGCTATCGCTAAGAAAGCGATGGCGCGTAAAACCGGTGCCCGTGGCCTGCGTTCCATCGTAGAAGCCGCACTGCTCGATACCATGTACGATCTGCC  >  NZ_CP009273/453777‑454044

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑