New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1660749 =	221 (1.160)	12 (0.070)	11/142	NT	6.2%	coding (560/1464 nt)	gluP	Rhomboid protease GluP
	?	USA300TCH1516_ALE	1660775 =	166 (0.980)					coding (534/1464 nt)	gluP	Rhomboid protease GluP

GAAATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1660847‑1660749 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaattattTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  >  USA300TCH1516_ALE/1660775‑1660864                                                                                                                                                                                               GAAATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTA                                                                                                    <  1:96363/91‑1 GAAATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTA                                                                                                    >  2:1140305/1‑91    ATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAA                                                                                                 <  2:896526/91‑1    ATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAA                                                                                                 <  1:2637627/91‑1     TTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAAT                                                                                                >  1:2326254/1‑91      ttcCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATT                                                                                               >  2:1981693/4‑91      TTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATT                                                                                               >  1:1083749/1‑91      TTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATT                                                                                               >  2:1982164/1‑91      TTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATT                                                                                               >  2:1982100/1‑91      TTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATT                                                                                               >  2:1982018/1‑91       TTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAATATTA                                                                                              >  1:1098431/1‑91       TTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTA                                                                                              >  1:1230621/1‑91        TCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             >  1:1736564/1‑91        TCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             >  2:175400/1‑91        TCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             >  1:978177/1‑91        TCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             >  2:2104795/1‑91        TCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             <  2:2166306/91‑1         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:32424/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:3766184/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:494169/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:493791/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:3767009/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  1:320415/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            <  1:2688334/91‑1         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT                                                                                            >  2:1866209/1‑91         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             <  1:2431787/90‑1         CACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTAT                                                                                             >  2:2431787/1‑90         CACCGGCAACATACACAATAATATTTGTAAACGTCTTAATATGGTTATGTATGATTTTATATTTAAAGAATTTTTCGGAGGTAAAATTATT                                                                                            >  2:2957622/1‑91         CACCGGCAACATACACAATAATATTTGTAAAAGTCTTAATATGGTTATGTATGATTTTATATTTAAACAATTTTTCGGATGTAAAATTATT                                                                                            >  2:2963189/1‑91                 ACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATA                                                                                    <  1:2572808/91‑1                 ACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATA                                                                                    <  2:3879174/91‑1                   ATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATAAA                                                                                  <  1:869426/91‑1                      CACAATTATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATAAAATC                                                                               <  2:412825/91‑1                               ATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATAAAATCATACATAAC                                                                      <  2:3693531/91‑1                                           CTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTACATCCGAAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACA                                                          <  1:2889855/91‑1                                                          TATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATTTAAATATAAAATCATACATAACAATATTAAGACATTTACAAAAAATATa                                           >  2:2304905/1‑90                                                                     ATTTAAATAATTTTTCGGATGTAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGC                                >  1:3044700/1‑91                                                                      TTTAAATAATTTTTCGGATGTAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCC                               >  2:47301/1‑91                                                                            TAATTTTTCGGATGTAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAA                         >  1:3297481/1‑91                                                                                   TCGGATGTAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCT                  >  2:2473644/1‑91                                                                                    CGGATGTAAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTG                 >  2:3260049/1‑91                                                                                           AAAATTATTTAGATATAAAATCAGACATAACCATATTAAGACATTTACAAATATTATTGCGTATGTTGCCGGTGAAAATTTCTGCATATAT          <  2:2958602/91‑1                                                                                           AAAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATAT          <  2:272503/91‑1                                                                                            AAATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATT         >  2:2301412/1‑91                                                                                             AATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTT        <  1:610680/91‑1                                                                                             AATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTT        >  1:1202046/1‑91                                                                                             AATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTT        >  1:1201972/1‑91                                                                                              ATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTA       <  1:695221/91‑1                                                                                              ATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTA       <  1:695213/91‑1                                                                                              ATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTA       >  2:725537/1‑91                                                                                              ATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTA       >  1:1293525/1‑91                                                                                              ATTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTA       >  2:2254128/1‑91                                                                                               TTATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATACTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTAT      >  2:2653981/1‑91                                                                                                TATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATC     <  1:372407/91‑1                                                                                                TATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATC     <  2:2146131/91‑1                                                                                                TATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATC     >  2:1696898/1‑91                                                                                                 ATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCT    >  2:2327859/1‑91                                                                                                 ATTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCT    >  2:2646006/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:1067058/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  2:965835/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:3725214/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:2685359/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:1970491/1‑91                                                                                                  TTTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:1067079/1‑91                                                                                                  TTTAAAGATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTA   >  1:3019532/1‑91                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  >  2:1040177/1‑91                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  >  2:1039850/1‑91                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  <  2:3631938/91‑1                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  <  1:3542437/91‑1                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  <  1:2338921/91‑1                                                                                                   TTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  <  1:1186122/91‑1                                                                                                                                                                                               GAAATTTTCACCGGCAACATACACAATAATATTTGTAAATGTCTTAATATGGTTATGTATGATTTTATATTTAAATAATTTTTCGGATGTAAAATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1660847‑1660749 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaattattTAAATATAAAATCATACATAACCATATTAAGACATTTACAAATATTATTGTGTATGTTGCCGGTGAAAATTTCTGCATATATTTATCTAA  >  USA300TCH1516_ALE/1660775‑1660864

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.