New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1980876	132 (0.690)	17 (0.100)	8/140	NT	13.7%	intergenic (‑118/+61)	USA300HOU_RS09865/USA300HOU_RS09870	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1980902	98 (0.590)					intergenic (‑144/+35)	USA300HOU_RS09865/USA300HOU_RS09870	hypothetical protein/hypothetical protein

ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1980777‑1980876 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagcgatgTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATTAA  <  USA300TCH1516_ALE/1980902‑1980814                                                                                                                                                                                               ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAA                                                                                                    >  2:3808015/1‑91 ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAA                                                                                                    <  1:1696319/91‑1 ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAA                                                                                                    <  2:3034637/91‑1 ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAA                                                                                                    >  2:1378361/1‑91   AACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCCATTTATTATTAGTTTACGTACAAAA                                                                                                  >  2:3459303/1‑91   AACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAA                                                                                                  >  1:289972/1‑91   AACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAA                                                                                                  >  1:2402968/1‑91      ATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGC                                                                                               <  2:2549839/91‑1       TAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCG                                                                                              <  2:888208/91‑1       TAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCG                                                                                              <  1:1989915/91‑1       TAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTAAATAAAAAAAGCG                                                                                              <  2:1535205/91‑1        AGTTATTCATTATACCACTATTTTTATTTTTTATTTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:522614/1‑91        AGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:2167146/1‑91        AGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:2167618/1‑91        AGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:916006/1‑91        AGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:438122/1‑91        AGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGA                                                                                             >  1:437878/1‑91         GTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGAT                                                                                            <  2:2289671/91‑1         GTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGAT                                                                                            <  2:1373678/91‑1                                    TTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGG                                                                 <  1:259629/91‑1                                      TTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCA                                                               <  1:1881054/91‑1                                      TTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATGAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCA                                                               <  2:905170/91‑1                                       TAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCAT                                                              <  2:3523953/91‑1                                       TAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCAT                                                              <  2:3643639/91‑1                                        AATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATC                                                             <  1:1623101/91‑1                                        AATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATC                                                             <  1:1622852/91‑1                                         ATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCG                                                            <  1:2012261/91‑1                                         ATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCG                                                            <  1:3658843/91‑1                                          TTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGC                                                           <  1:2030152/91‑1                                          TTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGC                                                           <  1:2030487/91‑1                                          TTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGC                                                           <  1:2030597/91‑1                                          TTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGC                                                           <  1:714876/91‑1                                          TTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTATTTCGAGAGGTGAGGCATCGC                                                           <  2:1571432/91‑1                                           TCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCT                                                          <  2:3309083/91‑1                                                AATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTG                                                     <  1:2590665/91‑1                                                AATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTG                                                     <  1:2590687/91‑1                                                                                           AAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAA          >  2:1361930/1‑91                                                                                           AAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAA          <  1:2424634/91‑1                                                                                           AAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAA          <  2:1454424/91‑1                                                                                           AAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAA          >  1:3864654/1‑91                                                                                           AAAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAA          >  1:2689400/1‑91                                                                                            AAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAAT         >  2:3098514/1‑91                                                                                            AAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAAT         >  2:3098370/1‑91                                                                                            AAAGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAAT         >  2:3098197/1‑91                                                                                              AGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGA       >  2:1053821/1‑91                                                                                              AGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGA       <  1:1180218/91‑1                                                                                              AGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGA       >  2:3624666/1‑91                                                                                              AGCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGA       >  2:2532411/1‑91                                                                                               GCGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAA      <  2:3221843/91‑1                                                                                                CGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAAT     >  2:2116578/1‑91                                                                                                CGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAAT     >  1:1766356/1‑91                                                                                                CGATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAAT     >  1:1766605/1‑91                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    >  1:1121229/1‑91                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    >  2:2036090/1‑91                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    >  2:2036168/1‑91                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    <  1:2643566/91‑1                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    <  1:828265/91‑1                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    <  1:3747494/91‑1                                                                                                 GATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATT    <  1:2643751/91‑1                                                                                                  ATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATTc   >  2:3855417/1‑90                                                                                                  ATGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATTA   <  1:2170451/91‑1                                                                                                   TGTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATTAA  <  1:2525045/91‑1                                                                                                                                                                                               ACAACATAGTTATTCATTATACCACTATTTTTATTTTTTAATTCATTAATCATTTCACTTTCTGCTCAATTTATTATTAGTTTACATACAAAAAGCGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1980777‑1980876 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagcgatgTAACACACCTGTTTCGAGAGGTGAGGCATCGCTTTTTGTATGTAAACTAATAATAAATTGAGCAGAAAGTGAAATGATTAATGAATTAA  <  USA300TCH1516_ALE/1980902‑1980814

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.