New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	42564 =	378 (1.060)	21 (0.080) +TACATTATAAAATACATATC	7/120	NT	6.9%	coding (1402/1524 nt)	USA300TCH1516_00035	hypothetical protein
	?	USA300TCH1516_ALE	1803072 =	NA (NA)					coding (796/807 nt)	USA300HOU_RS12765	hypothetical protein

ATGGCACTTAATATAAGAAAAGTAGTAGCTCAACGAGCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/42603‑42564 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTAT  >  USA300TCH1516_ALE/1803072‑1803156                                         ||||||||||||||||||||                                                                                      ATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATA                                                        <  1:2681604/91‑1  TGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAG                                                       <  2:2729527/91‑1   GGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATgga                                                      <  1:164538/91‑4   GGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATgga                                                      <  2:492935/91‑4   GGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGA                                                      <  1:3969853/91‑1    GCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAA                                                     <  1:4635499/91‑1     caaTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAA                                                    <  2:5943389/88‑1     CACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAA                                                    <  1:6076361/91‑1      ACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTATTTATTTGATAGAAAT                                                   <  2:1829042/91‑1      ACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAAT                                                   <  2:3079711/91‑1       aTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATC                                                  <  2:1620590/90‑1       CTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATC                                                  <  2:6090229/91‑1       CTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATC                                                  <  1:5230111/91‑1       CTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATC                                                  <  1:5230057/91‑1       CTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATC                                                  <  2:2590843/91‑1       CTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATC                                                  <  2:3550177/91‑1        TTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATCA                                                 <  1:5416872/91‑1         TAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATCAG                                                <  2:523652/91‑1          AATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGC                                               <  1:1813071/91‑1             ATAAGGAAAATAGCAGCGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATCAGCTTT                                            <  2:4149730/91‑1              TAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTT                                           <  1:3448314/91‑1                                              TATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTG           <  1:4358370/91‑1                                                    ATACATATCAAAAAAGCTGATTTCTATCAAATAAATAATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGC     >  1:358569/1‑91                                                       CATATCAAAAAAGCTGATTTCTATTAATTATTTGATGGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGGGCTGCTAT  <  2:598220/91‑1                                         ||||||||||||||||||||                                                                                      ATGGCACTTAATATAAGAAAAGTAGTAGCTCAACGAGCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/42603‑42564 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTAT  >  USA300TCH1516_ALE/1803072‑1803156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.