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%	169.7 / NA	49	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/34);  total (15/34)

CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACA  >  NZ_CP009273/1392741‑1392898                                                                                      |                                                                         cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                      <  2:239559/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  1:76467/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  1:975718/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:145342/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:613742/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:530128/90‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  1:25730/90‑1 (MQ=255)        gaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTg                                                               >  1:1064186/1‑90 (MQ=255)             cATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAg                                                          <  2:834114/90‑1 (MQ=255)                 gATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                      <  1:598452/90‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                      <  2:635653/70‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCtggctggt                                                                      >  1:635653/1‑70 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                      <  2:786956/86‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                      >  1:786956/1‑86 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:260500/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:213832/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:1192081/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:1059448/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:1090810/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:861898/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  <  1:150139/90‑1 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:258794/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:307698/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  <  1:613772/90‑1 (MQ=255)                        aaaaaGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATaaca                                               <  2:69416/90‑1 (MQ=255)                             ggCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAg                                          <  2:586781/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                       <  1:310890/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                       <  2:266083/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                       >  2:434330/1‑90 (MQ=255)                                  tAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGt                                     <  2:931634/90‑1 (MQ=255)                                  tAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGt                                     <  2:718619/90‑1 (MQ=255)                                     ttttGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCt                                  <  2:819298/90‑1 (MQ=255)                                     ttttGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCt                                  <  1:243588/90‑1 (MQ=255)                                       ttGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGa                                >  2:841469/1‑90 (MQ=255)                                          ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             <  1:213832/90‑1 (MQ=255)                                          ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             <  2:941357/90‑1 (MQ=255)                                          ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             <  2:520605/90‑1 (MQ=255)                                          ccaccaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             <  1:222067/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  2:982148/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  2:861898/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  2:361430/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  1:550702/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  1:988090/90‑1 (MQ=255)                                            accaATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTAGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  1:439872/90‑1 (MQ=255)                                                    gTTGATGTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATAc                   <  2:423485/90‑1 (MQ=255)                                                          gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  2:697359/90‑1 (MQ=255)                                                          gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  2:258794/90‑1 (MQ=255)                                                          gTAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  1:703613/90‑1 (MQ=255)                                                                 aaCAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTac      >  2:607766/1‑90 (MQ=255)                                                                    aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             <  1:1189261/64‑1 (MQ=255)                                                                    aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                             >  2:1189261/1‑64 (MQ=255)                                                                     gCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaaca  >  2:777647/1‑90 (MQ=255)                                                                                      |                                                                         CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACA  >  NZ_CP009273/1392741‑1392898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑