Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,392,826	T→C	Q18Q (CAA→CAG)	uspE ←	universal stress protein UspE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,392,826	0	T	C	100.0%	79.5 / NA	22	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/15);  total (7/15)

TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAA  >  NZ_CP009273/1392739‑1392899                                                                                        |                                                                          ttCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATgctggctg                                                                         >  1:225530/1‑90 (MQ=255) ttCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggttg                                                                         >  1:331917/1‑90 (MQ=255)   cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                       <  2:418773/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                  <  2:521318/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                  <  1:4658/90‑1 (MQ=255)             gTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGtt                                                             <  2:429894/90‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                       >  2:577941/1‑70 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                       <  1:577941/70‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                   >  2:184132/1‑90 (MQ=255)                              aGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGa                                            <  2:305588/90‑1 (MQ=255)                                            ccaccaATCCGTTGATGTAAATAAACAGCCCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                              <  1:503962/90‑1 (MQ=255)                                              accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                            <  1:169528/90‑1 (MQ=255)                                              accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                            <  2:376392/90‑1 (MQ=255)                                              accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                            <  1:184132/90‑1 (MQ=255)                                              accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                            <  1:16083/90‑1 (MQ=255)                                                 aaTCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGc                         <  2:115598/90‑1 (MQ=255)                                                     cGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATa                     >  1:255564/1‑90 (MQ=255)                                                       ttGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACa                   <  2:406988/90‑1 (MQ=255)                                                         gATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAgg                 <  1:178065/90‑1 (MQ=255)                                                            gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc              <  2:580277/90‑1 (MQ=255)                                                                      aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac    >  2:532221/1‑90 (MQ=255)                                                                      aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac    >  2:567378/1‑90 (MQ=255)                                                                       gCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaaca   >  2:414555/1‑90 (MQ=255)                                                                        cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCtt         <  1:483942/83‑1 (MQ=255)                                                                        cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCtt         >  2:483942/1‑83 (MQ=255)                                                                           gccgcAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTAcaacaa  >  1:512393/1‑87 (MQ=255)                                                                           gccgcAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTAcaacaa  <  2:512393/87‑1 (MQ=255)                                                                                        |                                                                          TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAA  >  NZ_CP009273/1392739‑1392899

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑