New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 278640	178 (0.870)	24 (0.130)	8/140	NT	13.2%	intergenic (+235/+79)	USA300HOU_RS01215/gsiB	hypothetical protein/Glutathione‑binding protein GsiB
	?	USA300TCH1516_ALE	= 278661	161 (0.900)					intergenic (+256/+58)	USA300HOU_RS01215/gsiB	hypothetical protein/Glutathione‑binding protein GsiB

TATAAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/278541‑278640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccacgccGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATTA  <  USA300TCH1516_ALE/278661‑278572                                                                                                                                                                                                TATAAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTA                                                                                                     >  1:2704992/1‑91  ATAAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAA                                                                                                    <  1:1591533/91‑1    AAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGTAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAAC                                                                                                  >  2:866998/1‑91    AAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAAC                                                                                                  >  1:394483/1‑91    AAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAAC                                                                                                  >  2:2686599/1‑91    AAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAAC                                                                                                  >  1:1892824/1‑91    AAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAAC                                                                                                  >  2:1089095/1‑91     AAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACC                                                                                                 >  1:292779/1‑91      AATGAACATGATTCACTGAAAGTATGTAATAATCATTATATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTCAACCA                                                                                                >  1:3675741/1‑91       ATGAACATGATTCACTGAAAGTATTTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCAC                                                                                               <  1:2420230/91‑1       ATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCAC                                                                                               <  1:2028205/91‑1       ATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCAC                                                                                               <  1:1946164/91‑1       ATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCAC                                                                                               <  1:653275/91‑1       ATGAACATGATTCACTGAAAGTATATAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCAC                                                                                               <  2:3664871/91‑1         GAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGC                                                                                             >  2:1699013/1‑91         GAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGC                                                                                             >  2:601260/1‑91          tACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCC                                                                                            >  2:1113010/2‑91          AACATGATTCACTGAGAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATGAATACAATCATATAGGCAAATTAAACCACGCC                                                                                            >  1:3379076/1‑91          AACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAACCCACGCC                                                                                            >  2:3581156/1‑91          AACATGATTCACTGAAAGTACGTAATAATCCTTTTATTGTAATTCATCAAACAGAAATTAATACAATCATATAAGCCACTTAAACCACCCC                                                                                            >  2:817942/1‑91                             ATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATT                                                                         <  2:796180/91‑1                             ATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATT                                                                         <  2:796151/91‑1                             ATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATT                                                                         <  2:796165/91‑1                              TGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTA                                                                        <  2:2095915/91‑1                              TGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTA                                                                        <  1:1705814/91‑1                              TGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTA                                                                        <  1:2312794/91‑1                              TGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTA                                                                        <  2:2327441/91‑1                               GTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTAT                                                                       <  1:1755168/91‑1                                TAATAATCATTTTATTGAAATTCATCAAACAGAAGTTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATG                                                                      <  2:2992409/91‑1                                TAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATG                                                                      <  2:2323631/91‑1                                TAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATG                                                                      <  1:1636268/91‑1                                 AATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCGTCCAATATGATTATGG                                                                     <  2:1248520/91‑1                                 AATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGG                                                                     <  1:3247211/91‑1                                 AATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGG                                                                     <  1:1584221/91‑1                                   TAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAGTTAAACCGCGCCGAAGTCATCCAATATGATTATGGCG                                                                   <  2:1117807/91‑1                                   TAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCG                                                                   <  2:2428801/91‑1                                   TAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCG                                                                   <  1:2121458/91‑1                                   TAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCG                                                                   <  2:1117546/91‑1                                    AATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGT                                                                  <  1:3836912/91‑1                                     ATCATTTTATTGAAATTCATCAAACAGAAATTAGTACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGTG                                                                 <  1:3234880/91‑1                                     ATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGTG                                                                 <  1:583833/91‑1                                     ATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGTG                                                                 <  1:74886/91‑1                                     ATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGTG                                                                 <  1:74918/91‑1                                     ATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCCGAAGTCATCCAATATGATTATGGCGTG                                                                 <  1:2230988/91‑1                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           >  1:1211951/1‑91                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           >  1:1211939/1‑91                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           <  1:1847770/91‑1                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           >  1:749468/1‑91                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           >  1:749453/1‑91                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           <  1:2715512/91‑1                                                                                           AAACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAA           <  1:3772086/91‑1                                                                                            AACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGCTGAATTTCAATAAAAT          >  2:3781141/1‑91                                                                                            AACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAAT          >  1:674190/1‑91                                                                                            AACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAAT          <  1:2066889/91‑1                                                                                            AACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAAT          >  1:3922197/1‑91                                                                                            AACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTCTGATGAATTTCAATAAAAT          <  2:3457548/91‑1                                                                                             ACCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTACTTTCTGTTTGATGAATTTCAATAAAATt         >  2:3438777/1‑90                                                                                              CCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGA        >  1:868712/1‑91                                                                                              CCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGA        >  2:3311397/1‑91                                                                                              CCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGA        >  2:2856799/1‑91                                                                                              CCACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTGATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGA        >  2:3551719/1‑91                                                                                               CACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGAT       <  1:648611/91‑1                                                                                               CACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGAT       <  1:893540/91‑1                                                                                                ACGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATT      <  2:3530862/91‑1                                                                                                 CGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTA     >  2:3938143/1‑91                                                                                                 CGCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTA     >  1:2943364/1‑91                                                                                                  GCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTAT    >  1:3533007/1‑91                                                                                                  GCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTAT    >  2:702552/1‑91                                                                                                  GCCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTAT    >  2:986208/1‑91                                                                                                   CCGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATT   >  1:2326936/1‑91                                                                                                   CCGAAGTCATCCAATATGATTATGGCGTGGTTTAACTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATT   >  2:1297630/1‑91                                                                                                    CGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATTA  >  2:3332946/1‑91                                                                                                    CGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATTA  <  1:3890859/91‑1                                                                                                    CGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATTA  >  1:563034/1‑91                                                                                                                                                                                                TATAAAATGAACATGATTCACTGAAAGTATGTAATAATCATTTTATTGAAATTCATCAAACAGAAATTAATACAATCATATAAGCAAATTAAACCACGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/278541‑278640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccacgccGAAGTCATCCAATATGATTATGGCGTGGTTTAATTTGCTTATATGATTGTATTAATTTCTGTTTGATGAATTTCAATAAAATGATTATTA  <  USA300TCH1516_ALE/278661‑278572

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.