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%	123.6 / NA	35	Q18Q (CAA→CAG)	uspE	universal stress protein UspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/20);  total (15/20)

CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACT  >  NZ_CP009273/1392741‑1392901                                                                                       |                                                                            cGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCtggctggt                                                                         <  1:598552/90‑1 (MQ=255)  gTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGgtc                                                                        <  1:91569/90‑1 (MQ=255)      gtgaAGTCATAGATCGGTAAAAAGGCTTTAATTTTGCCTCTAATCCGTTGATGT‑AAATAAACAGCTCGCCCCCATGCTGGCTGGTCGTcc                                                                    <  1:158454/88‑1 (MQ=255)      gagaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                    <  2:247648/90‑1 (MQ=255)       agaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGTAAAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTcc                                                                    <  2:53556/90‑1 (MQ=255)        gaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTg                                                                  >  2:589110/1‑90 (MQ=255)        gaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTg                                                                  >  1:37310/1‑90 (MQ=255)        gaAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTg                                                                  >  1:413689/1‑90 (MQ=255)           gTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGtt                                                               <  2:401393/90‑1 (MQ=255)             cATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAg                                                             >  2:661118/1‑90 (MQ=255)                 gATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATc                                                         <  2:722626/90‑1 (MQ=255)                    cGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGAt                                                      >  1:325839/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                     >  1:726217/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                     >  1:33313/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                     >  1:209534/1‑90 (MQ=255)                     ggCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATa                                                     >  2:530298/1‑90 (MQ=255)                           aaGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACg                                               <  1:156387/90‑1 (MQ=255)                           aaGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACg                                               >  2:25535/1‑90 (MQ=255)                              gCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGc                                            <  1:589110/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCTTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                          <  1:163777/90‑1 (MQ=255)                                tttAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                          >  2:529842/1‑90 (MQ=255)                                          ccaccaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                <  2:556258/90‑1 (MQ=255)                                          ccaccaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                <  1:530298/90‑1 (MQ=255)                                          ccaccaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATAc                                <  2:34114/90‑1 (MQ=255)                                           caccaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACa                               <  2:244604/90‑1 (MQ=255)                                            accaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACAt                              <  2:325839/90‑1 (MQ=255)                                             ccaATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATa                             >  2:649796/1‑90 (MQ=255)                                                          gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                <  1:25535/90‑1 (MQ=255)                                                          gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                <  1:181311/90‑1 (MQ=255)                                                          gT‑AAATAAACAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGtc                <  1:577962/90‑1 (MQ=255)                                                                taaaCAGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCtt           <  2:627104/90‑1 (MQ=255)                                                                     aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                          >  2:362110/1‑54 (MQ=255)                                                                     aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCAt                                          <  1:362110/54‑1 (MQ=255)                                                                     aGCTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTacaac      >  2:193854/1‑90 (MQ=255)                                                                       cTCGCCGCAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTAcaacaa    >  2:279757/1‑90 (MQ=255)                                                                         cgccgcAATGCTGGCTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACt  <  1:709852/90‑1 (MQ=255)                                                                                       |                                                                            CGTATGAGAAGTCATAGATCGGCAAAAAGGCTTTAATTTTGCCACCAATCCGTTGATGT‑AAATAAACAGCTCGCCGCAATGCTGGTTGGTCGTCCTGGTTAGGATCGATAACAACGAGCATGTTCTGATACATAGCCATACAGGGTCTCCTTACAACAACT  >  NZ_CP009273/1392741‑1392901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑