Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,728,024	A→C	S315S (TCA→TCC)	xylH →	xylose ABC transporter permease XylH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,728,024	0	A	C	100.0%	84.8 / NA	26	S315S (TCA→TCC)	xylH	xylose ABC transporter permease XylH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (15/11);  total (15/11)

ACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCG  >  NZ_CP009273/3727937‑3728109                                                                                        |                                                                                      aCGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTcccc                                                                                     <  1:289523/90‑1 (MQ=255)    cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc                                                                                  >  1:389732/1‑90 (MQ=255)    cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc                                                                                  >  2:171119/1‑90 (MQ=255)      ccAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTg                                                                                <  2:251207/90‑1 (MQ=255)             tGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGaaa                                                                         >  1:75437/1‑90 (MQ=255)              gCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAat                                                                        >  1:119165/1‑90 (MQ=255)                   gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc                                                                   <  2:54740/90‑1 (MQ=255)                   gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc                                                                   >  1:54740/1‑90 (MQ=255)                             aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc                                                         <  2:465545/90‑1 (MQ=255)                               cGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGc                                                       <  1:399841/90‑1 (MQ=255)                                  aTTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAAt                                                    >  2:361841/1‑90 (MQ=255)                                        ggTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcagc                                              <  2:125505/90‑1 (MQ=255)                                           aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg                                           >  2:449628/1‑90 (MQ=255)                                           aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg                                           >  2:295693/1‑90 (MQ=255)                                               aTCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTg                                       >  1:237235/1‑90 (MQ=255)                                                tCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGa                                      >  2:97704/1‑90 (MQ=255)                                                     ggATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTggc                                 <  2:71566/90‑1 (MQ=255)                                                      gATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTggcg                                >  2:444451/1‑90 (MQ=255)                                                          aaTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAc                            <  1:449628/90‑1 (MQ=255)                                                               ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGcc                       <  1:302099/90‑1 (MQ=255)                                                                    tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag                                               >  1:57916/1‑61 (MQ=255)                                                                    tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag                                               <  2:57916/61‑1 (MQ=255)                                                                      tcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGTCGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggctgg                <  2:265483/90‑1 (MQ=255)                                                                      tcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggctgg                >  1:514476/1‑90 (MQ=255)                                                                                   ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc   >  2:14937/1‑90 (MQ=255)                                                                                   ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc   >  2:507669/1‑90 (MQ=255)                                                                                    gTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCg  <  2:119165/90‑1 (MQ=255)                                                                                        |                                                                                      ACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCG  >  NZ_CP009273/3727937‑3728109

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑