Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,960,176	G→A	R540W (CGG→TGG)	ptsP ←	phosphoenolpyruvate‑‑protein phosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,960,176	0	G	A	100.0%	113.7 / NA	30	R540W (CGG→TGG)	ptsP	phosphoenolpyruvate‑‑protein phosphotransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/13);  total (17/13)

ACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCGTACGCAAGGTGAC  >  NZ_CP009273/2960042‑2960311                                                                                                                                       |                                                                                                                                        aCCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACAcc                                                                                                                                     >  1:135063/1‑139 (MQ=255) aCCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACAcc                                                                                                                                     <  2:383302/139‑1 (MQ=255)                gACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGAtc                                                                                                                      >  1:1960/1‑139 (MQ=255)                 aCTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGAtct                                                                                                                     <  1:95191/139‑1 (MQ=255)                    tCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCg                                                                                                                  >  2:179777/1‑139 (MQ=255)                     cACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCgg                                                                                                                 >  1:521424/1‑139 (MQ=255)                       cGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCt                                                                                                               >  1:468227/1‑139 (MQ=255)                                               cgTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTTATCGAGCGTAATGCGAATCCCAc                                                                                       >  1:729774/1‑139 (MQ=255)                                                 tGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCacac                                                                                                                                      >  2:85362/1‑90 (MQ=255)                                                 tGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCacac                                                                                                                                      <  1:85362/90‑1 (MQ=255)                                                 tGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGc                                                                                     >  2:294708/1‑139 (MQ=255)                                                   cTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGcc                                                                                    <  2:468227/138‑1 (MQ=255)                                                   cTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGcc                                                                                    <  1:574625/138‑1 (MQ=255)                                                        tcaACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTTATCGAGCGTAATGCGAATCCCACGCCAACCCa                                                                              <  2:729774/139‑1 (MQ=255)                                                                aTCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGa                                                                      >  1:408875/1‑139 (MQ=255)                                                                aTCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGa                                                                      >  2:344491/1‑139 (MQ=255)                                                                   gAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGAtt                                                                    <  1:294708/138‑1 (MQ=255)                                                                         tgtgACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCg                                                             >  1:333810/1‑139 (MQ=255)                                                                                              atTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCaaga                                                                                                                           >  1:342878/1‑56 (MQ=255)                                                                                              atTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCaaga                                                                                                                           <  2:342878/56‑1 (MQ=255)                                                                                                 cAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAgctg                                      <  1:344491/138‑1 (MQ=255)                                                                                                 cAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAgctg                                      <  2:649292/138‑1 (MQ=255)                                                                                                   ggTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAgctgct                                    >  1:348674/1‑138 (MQ=255)                                                                                                     ttGCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTAt                                 >  1:697514/1‑139 (MQ=255)                                                                                                       gCCCGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCt                               >  2:771849/1‑139 (MQ=255)                                                                                                        cccGTAGCGGCATTAGCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCTGCATGTAAGGCAGCTGCTTATCTg                              <  1:532042/139‑1 (MQ=255)                                                                                                                       gCACGCAGCATCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCg               >  1:385095/1‑139 (MQ=255)                                                                                                                            cagcaTCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTcc                          >  2:264204/1‑123 (MQ=255)                                                                                                                            cagcaTCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTcc                          <  1:264204/123‑1 (MQ=255)                                                                                                                             agcaTCGCCCACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCGTACGCa         <  2:385095/139‑1 (MQ=255)                                                                                                                                    cccACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCGTACGCAAGGTGAc  >  1:287736/1‑139 (MQ=255)                                                                                                                                    cccACACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCGTACGCAAGGTGAc  <  1:179777/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                        ACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCATGTAAGGCAGCTGCTTATCTGCTCCGACATCCAGCGTACGCAAGGTGAC  >  NZ_CP009273/2960042‑2960311

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑