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%	147.2 / NA	44	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/32);  total (12/32)

TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACA  >  NZ_CP009273/1392739‑1392898                                                                                         |                                                                         ttCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATgctggctg                                                                        >  2:1127563/1‑90 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  1:460628/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:1219514/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:1005564/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  2:708496/90‑1 (MQ=255)        gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                 <  1:1127563/90‑1 (MQ=255)             gTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGtt                                                            <  1:1357017/90‑1 (MQ=255)             gTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGtt                                                            <  2:439284/90‑1 (MQ=255)              tCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTa                                                           >  1:987939/1‑90 (MQ=255)               cATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAg                                                          <  2:1516669/90‑1 (MQ=255)                 tAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGa                                                        <  1:941741/90‑1 (MQ=255)                      cGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGAt                                                   >  2:418927/1‑90 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                      <  2:683824/86‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                      >  1:683824/1‑86 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:1079411/1‑90 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:86053/1‑90 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:831594/1‑90 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  <  2:1384693/90‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  <  1:669374/90‑1 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  1:472219/1‑90 (MQ=255)                       ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:1574315/1‑90 (MQ=255)                        gCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATaa                                                 <  2:302796/90‑1 (MQ=255)                            aaaGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATaacaac                                             <  1:424956/90‑1 (MQ=255)                                 cTTTAATTTTGCCACCAATCCGTTGATGTAAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGc                                         <  2:1470799/90‑1 (MQ=255)                                 cTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCa                                        <  1:1094342/90‑1 (MQ=255)                                  tttAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                       <  2:1030345/90‑1 (MQ=255)                                      aTTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTc                                   <  2:925415/90‑1 (MQ=255)                                              accaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  2:896578/90‑1 (MQ=255)                                              accaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  1:1230452/90‑1 (MQ=255)                                              accaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                           <  1:249650/90‑1 (MQ=255)                                                 aaTCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGc                        <  1:1574315/90‑1 (MQ=255)                                                  aTCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGcc                       <  1:680636/90‑1 (MQ=255)                                                         gATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAgg                <  2:1389880/90‑1 (MQ=255)                                                         gATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAgg                <  1:1081937/90‑1 (MQ=255)                                                            gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  2:373759/90‑1 (MQ=255)                                                            gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  1:235656/90‑1 (MQ=255)                                                            gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  2:493347/90‑1 (MQ=255)                                                            gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  1:1167854/90‑1 (MQ=255)                                                            gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc             <  1:112930/90‑1 (MQ=255)                                                                    aaCAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTac      >  1:514600/1‑90 (MQ=255)                                                                       aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGc                        <  1:1456572/69‑1 (MQ=255)                                                                       aGCTCGCCGCAATGCTGGCTGGCCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGc                        >  2:1456572/1‑69 (MQ=255)                                                                        gCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaaca  >  2:535643/1‑90 (MQ=255)                                                                         cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  >  2:481062/1‑41 (MQ=255)                                                                         cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                  <  1:481062/41‑1 (MQ=255)                                                                                         |                                                                         TTCGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACA  >  NZ_CP009273/1392739‑1392898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑