New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1045832	29 (1.050)	5 (0.190)	3/248	NT	15.2%	intergenic (+9/+43)	USA300HOU_0988/menA	hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
	?	CP000730	= 1045855	28 (1.060)					intergenic (+32/+20)	USA300HOU_0988/menA	hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase

ACATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/1045691‑1045832 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actcgGCAATCGACTTACATCGAACTGTCGAGT  <  CP000730/1045855‑1045828                                                                                                                                                                            ACATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTAAAAAAAAAAAAAACTC                               <  2:332578/141‑1  CATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCG                              >  2:121389/1‑141                              TTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGGGGGACATATTGAATTATACAAGCACATGTATGATCATTTAATTGTTAAATAAACAAACTCGGCAATCGACTTACATCGAACTGTCGTGT  <  2:57908/141‑1                                                          TAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGGCAATCGACTTACATCGAACTGTC      <  1:143678/109‑1                                                          TAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGGCAATCGACTTACATCGAACTGTC      >  2:143704/1‑109                                                          TAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGGCAATCGACTTACATCGAACTGTC      <  1:143704/109‑1                                                          TAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGGCAATCGACTTACATCGAACTGTC      >  2:143678/1‑109                                                                                                                                                                            ACATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/1045691‑1045832 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actcgGCAATCGACTTACATCGAACTGTCGAGT  <  CP000730/1045855‑1045828

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ 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.