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%	61.3 / NA	20	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/14);  total (6/14)

TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACGC  >  NZ_CP009273/1392739‑1392909                                                                                        |                                                                                    ttCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATgctggctg                                                                                   >  2:53625/1‑90 (MQ=255)   cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                 <  1:35623/90‑1 (MQ=255)   cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                 <  1:452408/90‑1 (MQ=255)   cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                                 <  1:53625/90‑1 (MQ=255)          gaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTg                                                                          >  2:489997/1‑90 (MQ=255)             gTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGtt                                                                       <  2:385466/90‑1 (MQ=255)               cATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAg                                                                     <  1:142201/90‑1 (MQ=255)                 tAGATCGGCAAAAAGGCTTTAATTTTGCCCCCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGa                                                                   <  2:492737/90‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                            <  1:24744/75‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                            >  2:24744/1‑75 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                             >  1:584506/1‑90 (MQ=255)                                    tAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGt                                                <  2:310166/90‑1 (MQ=255)                                            ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                        <  1:462420/90‑1 (MQ=255)                                            ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                        <  2:487500/90‑1 (MQ=255)                                            ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                        <  1:242807/90‑1 (MQ=255)                                                 aaTCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGc                                   <  1:209346/90‑1 (MQ=255)                                                      gTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATAc                              >  1:219880/1‑90 (MQ=255)                                                            gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                        <  1:56979/90‑1 (MQ=255)                                                            gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                        <  2:282728/90‑1 (MQ=255)                                                            gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTACTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                        <  2:389008/90‑1 (MQ=255)                                                              aaataaaCAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtctc                      >  2:186486/1‑90 (MQ=255)                                                                         tCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATTAATAACAACGAGCATGTTCTGAGACATAGCCATACAGGGTCTCCTTACaacaac           >  1:579265/1‑90 (MQ=255)                                                                             cgcAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTc       <  2:584506/90‑1 (MQ=255)                                                                                  tGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACGc  <  1:73914/90‑1 (MQ=255)                                                                                        |                                                                                    TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACTGTCAACGC  >  NZ_CP009273/1392739‑1392909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑