New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1660030	102 (1.040)	9 (0.110)	5/138	NT	9.2%	coding (1279/1464 nt)	gluP	Rhomboid protease GluP
	?	USA300TCH1516_ALE	= 1660054	90 (1.060)					coding (1255/1464 nt)	gluP	Rhomboid protease GluP

ACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1659932‑1660030 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attctaagtccGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCATT  <  USA300TCH1516_ALE/1660054‑1659966                                                                                                                                                                                              ACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATT                                                                                                   <  1:2454921/91‑1  CGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTC                                                                                                  >  1:2248756/1‑91    CACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTA                                                                                                >  1:3823787/1‑91    CACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTA                                                                                                >  1:3823646/1‑91    CACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTA                                                                                                <  1:1890982/91‑1      CATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAG                                                                                              <  1:1152555/91‑1      CATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAG                                                                                              >  1:3649295/1‑91       ATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGT                                                                                             >  1:1878438/1‑91        TATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTC                                                                                            <  1:1316899/91‑1         ATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCC                                                                                           <  1:2436718/91‑1                             TCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGA                                                                       <  1:2754940/91‑1                                  TAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAG                                                                  <  1:1226277/91‑1                                  TAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAG                                                                  <  1:1010300/91‑1                                   AATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGG                                                                 <  1:3914977/91‑1                                   AATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGG                                                                 <  1:3101221/91‑1                                   AATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGG                                                                 <  1:3100972/91‑1                                      GAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACT                                                              <  1:2021614/91‑1                                         CGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAG                                                           <  1:93627/91‑1                                         CGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAG                                                           <  1:2398601/91‑1                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2247489/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           <  1:818911/91‑1                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:1505742/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2987916/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2987592/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2987281/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2305697/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2305762/1‑91                                                                                         ATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAA           >  1:2385365/1‑91                                                                                            CTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCG        >  1:2186782/1‑91                                                                                            CTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCG        <  1:4027497/91‑1                                                                                            CTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCG        <  1:3990593/91‑1                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       >  1:3705274/1‑91                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       <  1:4099906/91‑1                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       <  1:295229/91‑1                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       >  1:2407224/1‑91                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       <  1:1712564/91‑1                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       <  1:1712506/91‑1                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       >  1:3024865/1‑91                                                                                             TAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGT       >  1:3024164/1‑91                                                                                               AGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTC     >  1:1453363/1‑91                                                                                               AGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTC     >  1:3888601/1‑91                                                                                               AGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTC     >  1:3098579/1‑91                                                                                               AGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTC     >  1:3084705/1‑91                                                                                                GTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCA    >  1:25033/1‑91                                                                                                 TCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCAT   >  1:4037022/1‑91                                                                                                  CCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCATT  >  1:2632786/1‑91                                                                                                                                                                                              ACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1659932‑1660030 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attctaagtccGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCATT  <  USA300TCH1516_ALE/1660054‑1659966

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