Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,565	A→G	intergenic (‑587/‑119)	intD ← / → renD	putative integrase/protein RenD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,565	0	A	G	100.0%	57.4 / NA	19	intergenic (‑587/‑119)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (8/11);  total (8/11)

AAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTG  >  NC_000913/566391‑566797                                                                                                                                                                                |                                                                                                                                                                                                                                         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)                                                                                                                                                           gcgagaattAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAGGCGCAACAGTAAccagcataaatcaggccg       <  1:340592‑M1/245‑19 (MQ=255)                                                                                                                                                           gcgagaattAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACGTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACGTTGCCGCGCTAACAGGCGCAACAGTAAccagcataaatcaggccgcg     <  2:128643‑M1/247‑21 (MQ=255)                                                                                                                                                               gAATTAACCGTGGTGAGGCGATCCCTGAACCAGTAAAACAACTTCCTGTCATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATCAAAGCTAAGTTCGGACTGAAAGGAGCAAGAGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCGCCGGACTTTGCCGCGCTAACAGGCGCCACAGTAAccagcataaatcaggccgcggct  >  2:222820‑M1/1‑227 (MQ=255)                                                                                                                                                                                |                                                                                                                                                                                                                                         AAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTACCAACTTGTACCAGAACATGCGGGCCAATGCGCTGGCTGACGCGGAATTACGGCGCAAGGCTGCCGATGAACT‑GACCTGTATGACAGCGCGAATTAACCGTGGTGAGACGATACCTGAACCAGTAAAACAACTTCCTGTTATGGGCGGTAGACCTCTAAATCGTGCACAGGCTCTGGCGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTG  >  NC_000913/566391‑566797

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: ‑