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%	17.8 / NA	7	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (2/5);  total (2/5)

GAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTC  >  NZ_CP009273/1392746‑1392887                                                                                 |                                                              gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                      <  1:41800/90‑1 (MQ=255)        cATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAg                                               <  2:38461/90‑1 (MQ=255)          tAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGa                                             <  1:172841/90‑1 (MQ=255)             aTCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCg                                          >  1:168144/1‑90 (MQ=255)                ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                       >  1:143221/1‑90 (MQ=255)                           tttAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                            <  1:222752/90‑1 (MQ=255)                                                     gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc  <  2:70349/90‑1 (MQ=255)                                                                                 |                                                              GAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTC  >  NZ_CP009273/1392746‑1392887

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑