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%	69.6 / NA	21	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/11);  total (10/11)

CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACG  >  NZ_CP009273/1392741‑1392908                                                                                      |                                                                                   cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                <  2:833146/90‑1 (MQ=255) cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                <  1:495565/90‑1 (MQ=255) cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                <  2:544221/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                           <  2:536983/90‑1 (MQ=255)          aGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGt                                                                       >  2:800685/1‑90 (MQ=255)               tAGGTCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGa                                                                  <  2:801368/90‑1 (MQ=255)               tAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGa                                                                  <  2:680278/90‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                <  1:534109/70‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                >  2:534109/1‑70 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                            >  1:249105/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                            >  1:115809/1‑90 (MQ=255)                               cTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCa                                                  <  1:74090/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                                 >  2:510919/1‑90 (MQ=255)                                  tAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGt                                               <  1:886934/90‑1 (MQ=255)                                     ttttGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCt                                            <  2:763219/90‑1 (MQ=255)                                       ttGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGa                                          >  1:77795/1‑90 (MQ=255)                                          ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                       <  2:146551/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                                     <  1:800685/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                                     <  1:670712/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                                     <  1:428054/90‑1 (MQ=255)                                                                    aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac             >  2:237016/1‑90 (MQ=255)                                                                    aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac             >  2:619435/1‑90 (MQ=255)                                                                    aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac             >  1:659784/1‑90 (MQ=255)                                                                      cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTAcaacaa           <  2:249105/90‑1 (MQ=255)                                                                             cAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCaa    >  2:153416/1‑90 (MQ=255)                                                                               aTGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACg  >  1:570890/1‑90 (MQ=255)                                                                                      |                                                                                   CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACG  >  NZ_CP009273/1392741‑1392908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑