Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,199	4 bp→GAGG	intergenic (‑221/‑482)	intD ← / → renD	putative integrase/protein RenD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,199	0	T	G	100.0%	25.5 / NA	8	intergenic (‑221/‑485)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (6/2);  total (6/2)
*	NC_000913	566,200	0	T	A	100.0%	17.8 / NA	8	intergenic (‑222/‑484)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (6/2);  total (6/2)
*	NC_000913	566,201	0	T	G	100.0%	26.3 / NA	8	intergenic (‑223/‑483)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (6/2);  total (6/2)
*	NC_000913	566,202	0	C	G	100.0%	23.2 / NA	8	intergenic (‑224/‑482)	intD/renD	putative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (6/2);  total (6/2)

CCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCG‑CCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAG  >  NC_000913/566113‑566393                                                                                        ||||                                                                                                                                                                                                cccgaacgtgaagccgatctctgCCAGCGCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATg                                 >  1:511987/23‑250 (MQ=255)   cgaacgtgaagccgatctctgCCAGCGCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATGa                                >  2:127783/21‑249 (MQ=255)        gtgaagccgatctctgCCAGCGCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGAACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATGAAATcgcg                         >  2:201721/16‑248 (MQ=255)                     ctgCCAGCGCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCa                                   <  1:510295/226‑1 (MQ=255)                     ctgCCAGCGCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATGAAGTCGCGGGAGGtgaa                <  1:426560/245‑4 (MQ=255)                     ctgCCAGCGCCTCGTCCATATTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTCGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGCTGGCTTCGAAACCGCCAAGGCGGAATTTCa                                   >  2:510295/3‑228 (MQ=255)                            cgCCTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATGAAGTCGCGGGAGGtgaaagggcattta      >  1:282462/2‑237 (MQ=255)                               cTCGTCCATCTTCTCGATGAACTCCGGCACCATTTCGTTGAAA‑TCGGACATGTACTGAGGATCCCGCTCAACGACGACGTGGTGAATGCCTTCGCGTTTCATGCGCGGGTCGTAGTTTGCAAAGAACCATGCGTCTTTTCCGGTCACCCACATGCTGTACTGCACCTGGGCCATGTACGCAGACTTGATGGCTTCGAAACCGCCAAGGCGGAATTTCATGAAGTCGCGGGAGGtgcaagggcatttaagct  >  2:329988/1‑234 (MQ=255)                                                                                        ||||                                                                                                                                                                                                CCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCG‑CCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAG  >  NC_000913/566113‑566393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑