Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,413,020	(T)5→4	coding (216/1236 nt)	intR ←	Rac prophage; putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,016	0	T	.	100.0%	33.6 / NA	9	coding (220/1236 nt)	intR	Rac prophage; putative integrase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (5/4);  total (5/4)

TTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTAT  >  NC_000913/1412941‑1413088                                                                            |                                                                         ttAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCAttttgc                                                                     >  1:268911/1‑79 (MQ=255)      tctGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCA‑TTTTGCCCCAg                                                               >  1:268906/1‑81 (MQ=255)       ctGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTCATGACTCTCGTTGTCACCA‑TTTTGCCCCAGt                                                              >  2:268914/1‑81 (MQ=255)          tctcTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCA‑TTTTGCCCCAGTGc                                                            <  2:268892/80‑1 (MQ=255)                tAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTTGTTGTCACCA‑TTTTGCCCCAGTGCTGGACTg                                                     >  2:268907/1‑81 (MQ=255)                   tttttGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCA‑TTTTGCCCCAGTGCTGGACTgggg                                                  <  1:268893/81‑1 (MQ=255)                                   acaAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCA‑TTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATAc                                  <  2:268894/81‑1 (MQ=255)                                            tcCGAACGTTTTTATGACTCTCGTTGTCACCA‑TTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAAtt                           <  1:268895/79‑1 (MQ=255)                                                              tctcGTTGTCACCA‑TTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATg        >  2:268912/1‑80 (MQ=255)                                                                     gTCACCA‑TTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTAt  >  2:268927/1‑79 (MQ=255)                                                                            |                                                                         TTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTAT  >  NC_000913/1412941‑1413088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑