Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	281,837	C→A	Q49H (CAG→CAT)	yagA ←	CP4‑6 prophage; integrase core domain‑containing protein YagA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	281,837	0	C	A	100.0%	118.9 / NA	33	Q49H (CAG→CAT)	yagA	CP4‑6 prophage; integrase core domain‑containing protein YagA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (16/17);  total (16/17)

GCGGTTCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCT  >  NC_000913/281768‑281910                                                                      |                                                                          gCGGTTCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACtt                                                                >  2:59253/1‑81 (MQ=255)  cGGTTCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTg                                                               >  1:59254/1‑81 (MQ=255)   ggTTCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGt                                                              <  2:59193/81‑1 (MQ=255)     ttCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAg                                                            <  1:59194/81‑1 (MQ=255)     ttCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAg                                                            <  2:59195/81‑1 (MQ=255)          ggAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGt                                                       >  2:59260/1‑81 (MQ=255)          ggAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGt                                                       <  2:59196/81‑1 (MQ=255)              tGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCa                                                   <  1:59197/81‑1 (MQ=255)                gTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAgg                                                 >  2:59252/1‑81 (MQ=255)                  gCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGt                                                >  2:59257/1‑80 (MQ=255)                   cGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTg                                               <  1:59198/80‑1 (MQ=255)                       aTGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATg                                          <  1:59199/81‑1 (MQ=255)                            cgggcggTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGaa                                     <  1:59201/81‑1 (MQ=255)                            cgggcggTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGaa                                     <  1:59202/81‑1 (MQ=255)                            cgggcggTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGaa                                     <  1:59200/81‑1 (MQ=255)                             gggcggTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAg                                    >  2:59264/1‑81 (MQ=255)                                  gTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACg                               <  2:59203/81‑1 (MQ=255)                                   tCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACgg                              <  1:59204/81‑1 (MQ=255)                                     cTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACgg                              >  2:59243/1‑79 (MQ=255)                                       gAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCa                            >  2:59256/1‑79 (MQ=255)                                       gAAGACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCa                            >  1:59265/1‑79 (MQ=255)                                          gACCGGCGGCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAggg                       <  2:59205/81‑1 (MQ=255)                                             cggcggCACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAAc                    <  2:59206/81‑1 (MQ=255)                                              ggcggcACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACg                   >  2:59263/1‑81 (MQ=255)                                               gcggcACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACgg                  <  2:59207/81‑1 (MQ=255)                                               gcggcACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACg                   >  2:313659/1‑80 (MQ=255)                                                 ggcACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGAt                <  2:59208/81‑1 (MQ=255)                                                 ggcACCTTCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGAt                >  2:59255/1‑81 (MQ=255)                                                        tCCTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGcc         >  1:59258/1‑81 (MQ=255)                                                          cTGAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGcccc       >  2:59270/1‑81 (MQ=255)                                                            gAGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGt     >  2:59262/1‑81 (MQ=255)                                                             aGCCCAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCg      <  2:59209/79‑1 (MQ=255)                                                               cccAGCGATGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCt  >  1:59268/1‑81 (MQ=255)                                                                      |                                                                          GCGGTTCGGGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCT  >  NC_000913/281768‑281910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑