Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,547	C→A	intergenic (‑569/‑137)	intD ← / → renD	putative integrase/protein RenD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,547	0	C	A	100.0%	52.6 / NA	16	intergenic (‑569/‑137)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (7/9);  total (7/9)

AAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGT  >  NC_000913/566391‑566772                                                                                                                                                              |                                                                                                                                                                                                                                  aaGCGAGGCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAAGCAAACGCGCACTACTGGCTGGTTTCCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCTCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGAt                                                                                                                                     <  1:239453/251‑1 (MQ=255)     gaggCCTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATCTGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTAATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGGGAAGATCGc                                                                                                                                  >  2:340592/3‑250 (MQ=255)      aggacTGTATCCGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCTGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCGGGCGAAGATCGCAg                                                                                                                                <  2:3831/247‑1 (MQ=255)                ccGGATGCGGAGTCTTATCCGTGGAAATCAAACGCGCACTACTGGCGGGTTACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAga                                                                                                                      <  2:16900/251‑2 (MQ=255)                                                                gttACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAatt                                                                      <  1:218938/251‑1 (MQ=255)                                                                gttACCAACCTGTATCAGAACATGCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCGCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCGAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAatt                                                                      <  1:250210/251‑1 (MQ=255)                                                                          tGTATCAGAAGATGAGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGACCGCAGATAAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATAGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTAGGACTGAAAGGAGCAAGGGTATGACGGGCAAAGCGGCAATTATTAATTAcc                                                            >  2:255194/1‑251 (MQ=255)                                                                                     aggCGGGCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCAt                                                 <  2:240484/249‑1 (MQ=255)                                                                                           gCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGaa                                                                                                       >  1:196792/1‑191 (MQ=255)                                                                                           gCCAATGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGGCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAAGCAAAGCTAAGTTCGGACTGaa                                                                                                       <  2:196792/191‑1 (MQ=255)                                                                                              aaTGCGCTTACTGATGCGGAATTACGCCGTAAGGCCGCAGATGAGCTTGTCC‑ATATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTc                                        >  1:29763/1‑251 (MQ=255)                                                                                                                             aaggccgcagatgagcttgtccatATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTACGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAGgc          >  1:70041/24‑251 (MQ=255)                                                                                                                             aaggccgcagatgagcttgtccatATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAGgc          <  1:107533/228‑1 (MQ=255)                                                                                                                              aggccgcagatgagcttgtccatATGACTGCGAGAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGGGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAGgcg         <  2:70041/229‑1 (MQ=255)                                                                                                                                     agatgagcttgtccatATGACTGCGAGAATTACCCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTACCAGGCGCAAcagt  >  2:140430/16‑248 (MQ=255)                                                                                                                                           gcttgtccatATGACTGCGAGAATTAACCGTGGCGAGGCGATCCCTGAACCCGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACCGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGCCTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGCCGCATAATAGCTTCt                                       >  1:277025/10‑208 (MQ=255)                                                                                                                                                              |                                                                                                                                                                                                                                  AAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGT  >  NC_000913/566391‑566772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑