New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	19796 =	NA (NA)	6 (0.090)	6/240	4.4	7.6%	intergenic (‑1/+15)	BW25113_RS25960/BW25113_RS00100	fimbrial family protein/IS1‑like element IS1A family transposase
	?	NZ_CP009273	3370648 =	73 (1.140)					coding (132/639 nt)	sspA	stringent starvation protein A
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/19892‑19796 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCAT  >  NZ_CP009273/3370648‑3370749                                                                                                                                                                                                         GAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCT                                                               >  1:99865/1‑138   AGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAG                                                            >  2:88233/1‑139                   AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCG                                               <  2:99865/136‑1                                             TCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGAT                                       <  1:203024/118‑1                                             TCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGAT                                       >  2:203024/1‑118                                                             GAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCAT  >  1:720982/1‑139                                                                                                                                                                                                         GAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/19892‑19796 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCAT  >  NZ_CP009273/3370648‑3370749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ 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.