New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	48945 =	139 (1.350)	6 (0.060)	5/294	7.8	4.0%	intergenic (‑54/+180)	hin_2/USA300HOU_RS00205	DNA‑invertase hin/hypothetical protein
	?	USA300TCH1516_ALE	48974 =	151 (1.480)					intergenic (‑83/+151)	hin_2/USA300HOU_RS00205	DNA‑invertase hin/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ACTGAATAATCGACGTATTGAAGATAGAACAAATAACGGAGTGAAAAACATGGATGAACTTATCGAGATATTAGCCGATTTGGTAATTGAAGAAATCAATCAAACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/49093‑48945 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCAATACGTCGATTATTCAGTTTGATGCTTCACAGTTGTATGATAAAGA  >  USA300TCH1516_ALE/48974‑49121                                                                                                                                                                                                                                                                                                           ACTGAATAATCGACGTATTGAAGATAGAACAAATAACGGAGTGAAAAACATGGATGAACTTATCGAGATATTAGCCGATTTGGTAATTGAAGAAATCAATCAAACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCTT                                                                                                                                                      <  2:783714/149‑1                                             AAAACATGGATGAACTTATCGAGATATTAGCCGATTTGGTAATTGAAGAAATCAATCAAACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCTTCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATC                                                                                                          >  2:30397/1‑149                                                                                                TCAATCAAACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCGTCCATATTAGTCATTTGCTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTTCGTTATTTGTTCT                                                       >  1:71749/1‑149                                                                                                       AACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCTTCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCA                                                <  1:30397/149‑1                                                                                                                              CAACATCTCATTGATGTTGGGCGTCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCAATACGTCGATTATTCAGTTTGAT                         >  1:798338/1‑149                                                                                                                               AACATCTCATTGATGTTGGGCGTCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCAATACTTCGATTATTCAGTTTGATG                        >  2:893042/1‑149                                                                                                                               AACATCTCATTGATGTTGGGCGTCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCAATACGTCGATTATTCAGTTTGATG                        >  2:293124/1‑149                                                                                                                                                     TCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCCTGTTTTTCACTCCGTTATTTGTTCTATCTTCAAGACGTCGATTATTCAGTTTGATGCTTCACAGGTGTATGATAAAGA  >  2:728877/1‑149                                                                                                                                                     TCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGATTTTCACTCCGTTATTTGTTCTATCTTCAATACGTCGATTATTCAGTTTGATGCTTCACAGTTGTATGATAAAGA  >  2:405953/1‑149                                                                                                                                                     TCCATATTAGTCATTTGATTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGATTTTCACTCCGTTAGTTTTTCTATCTTCATTCACTCGATTATTCAGTTTGATGCTTCAACGTTGTATGctcacaa  >  2:495540/1‑142                                                                                                                                                                                                                                                                                                           ACTGAATAATCGACGTATTGAAGATAGAACAAATAACGGAGTGAAAAACATGGATGAACTTATCGAGATATTAGCCGATTTGGTAATTGAAGAAATCAATCAAACAAATGACTAATATGGACGCCCAACATCTCATTGATGTTGGGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/49093‑48945 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tCCATATTAGTCATTTGTTTGATTGATTTCTTCAATTACCAAATCGGCTAATATCTCGATAAGTTCATCCATGTTTTTCACTCCGTTATTTGTTCTATCTTCAATACGTCGATTATTCAGTTTGATGCTTCACAGTTGTATGATAAAGA  >  USA300TCH1516_ALE/48974‑49121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.