Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,414	A→G	intergenic (‑436/‑270)	intD ← / → renD	putative integrase/protein RenD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,414	0	A	G	100.0%	61.1 / NA	18	intergenic (‑436/‑270)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (8/10);  total (8/10)

GAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAAT  >  NC_000913/566379‑566650                                    |                                                                                                                                                                                                                                              gAGTATTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGc                       >  2:204776/1‑251 (MQ=255)  aGTATTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGct                      >  1:488219/1‑251 (MQ=255)   gTATTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGctc                     >  2:632187/1‑251 (MQ=255)     aTTGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGctct                    <  2:259564/250‑1 (MQ=255)       tGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTgg                  <  1:462559/250‑1 (MQ=255)       tGCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTGCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTgg                  <  2:78471/250‑1 (MQ=255)        gCCGGAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGc                 <  2:306055/250‑1 (MQ=255)          cGGAAGCGAGGCCTGTATCCGGATGCGGATTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGaa              <  1:683086/251‑1 (MQ=255)           ggAAGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGa               >  1:369015/1‑249 (MQ=255)             aaGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGa               >  1:439590/1‑247 (MQ=255)             aaGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGAt           <  2:488219/251‑1 (MQ=255)              aGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATc          <  1:292604/251‑1 (MQ=255)                 gaggCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGc        >  1:203766/3‑250 (MQ=255)                  aggCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAg      <  1:220887/250‑1 (MQ=255)                   ggCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGc        >  1:240016/1‑248 (MQ=255)                    gCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAACACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGa     >  2:416052/1‑250 (MQ=255)                        gTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTTGCGAAGATCGCTGAAAt  <  2:311179/249‑1 (MQ=255)                        gTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAAt  <  2:402282/249‑1 (MQ=255)                                    |                                                                                                                                                                                                                                              GAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAAT  >  NC_000913/566379‑566650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑