Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_000913	1,433,862	0	C→A	100.0%	0.8	1	intergenic (‑188/+129)	pinR/ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (1/0):  ref base (0/0):  total (1/0)

AGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGG  >  NC_000913/1433657‑1433866                                                                                                                                                                                                              |     aGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTACggg  >  2:148990/1‑210 (MQ=14)                                                                                                                                                                                                              |     AGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGG  >  NC_000913/1433657‑1433866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.