New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1361481	142 (0.750)	22 (0.130)	12/140	NT	12.8%	intergenic (+20/+273)	USA300HOU_RS06765/USA300TCH1516_01271	Putative phosphatase/hypothetical protein
	?	USA300TCH1516_ALE	= 1361509	176 (1.060)					intergenic (+48/+245)	USA300HOU_RS06765/USA300TCH1516_01271	Putative phosphatase/hypothetical protein

AACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1361382‑1361481 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagccttaacCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTCATT  <  USA300TCH1516_ALE/1361509‑1361420                                                                                                                                                                                                AACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATA                                                                                                     >  2:1466390/1‑91 AACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATA                                                                                                     >  1:2842544/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  2:1422429/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  2:3036517/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  2:3311847/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  2:3508718/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    <  2:3527245/91‑1  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  1:2707181/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  1:2706653/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  1:2630095/1‑91  ACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAA                                                                                                    >  1:2629838/1‑91    TTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGC                                                                                                  >  2:2396780/1‑91    TTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGC                                                                                                  <  1:129868/91‑1      AAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCT                                                                                                <  2:3039841/91‑1       AGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTT                                                                                               <  2:1798930/91‑1        GCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTA                                                                                              >  1:1880068/1‑91          AATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAAC                                                                                            <  1:2840274/91‑1          AATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAAC                                                                                            >  2:3019759/1‑91                              TTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAA                                                                        <  2:32895/91‑1                                      TAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGT                                                                <  2:1794684/91‑1                                          GAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTA                                                            <  1:717952/91‑1                                          GAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTA                                                            <  2:1039624/91‑1                                           AAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAA                                                           <  2:1279387/91‑1                                           AAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAA                                                           <  1:1738884/91‑1                                           AAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAA                                                           <  1:2002525/91‑1                                            AAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAG                                                          <  1:2073886/91‑1                                            AAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAG                                                          <  1:2072496/91‑1                                             AATGGTATTCCACATGCGCTCAAAAGATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGG                                                         <  2:3362329/91‑1                                                 GTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTA                                                     <  2:426214/91‑1                                                 GTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTA                                                     <  2:2084354/91‑1                                                 GTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTA                                                     <  2:2083192/91‑1                                                   ATTCCACACGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATT                                                   <  2:273019/91‑1                                                     TCCACATGCGCTCAAAAAATTGTTAGAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTT                                                 <  1:1182416/91‑1                                                       CACATTCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAA                                               <  2:3578240/91‑1                                                       CACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAA                                               <  1:3818589/91‑1                                                       CACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAA                                               <  2:3373762/91‑1                                                       CACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAA                                               <  1:3664127/91‑1                                                       CACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAA                                               <  1:1055136/91‑1                                                              GCTCAAAAAATTGTTATAAATTGTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTAT                                        <  2:3124612/91‑1                                                                                  TTTTAAAATAAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATG                    <  1:1252162/91‑1                                                                                           AAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACC           >  2:829158/1‑91                                                                                           AAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACC           <  2:3524160/91‑1                                                                                           AAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACC           >  2:2785672/1‑91                                                                                           AAGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACC           >  1:1128397/1‑91                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  2:2586197/91‑1                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  2:3312939/91‑1                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  2:2330992/91‑1                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  1:1270735/91‑1                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  2:2930992/91‑1                                                                                            AGCCTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTCTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCA          <  2:3199518/91‑1                                                                                               CTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTT       <  2:2546268/91‑1                                                                                               CTTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTT       <  2:3408155/91‑1                                                                                                TTAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTT      <  2:263832/91‑1                                                                                                 TAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTC     <  1:2103398/91‑1                                                                                                 TAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTC     <  1:1597616/91‑1                                                                                                 TAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTC     <  1:1596424/91‑1                                                                                                 TAACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTC     <  2:565719/91‑1                                                                                                   ACCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTCAT   >  1:853756/1‑91                                                                                                    CCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTCATT  <  1:718702/91‑1                                                                                                                                                                                                AACTTAAGCAATATGCAAATGAAGTTACGTTGGATCATAATGAAAATGGTATTCCACATGCGCTCAAAAAATTGTTATAAATTTTAAAATAAGCCTTAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1361382‑1361481 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagccttaacCACAAGATATCTTATTCAAATATCATGTGTTAAGGCTTATTTTAAAATTTATAACAATTTTTTGAGCGCATGTGGAATACCATTTTCATT  <  USA300TCH1516_ALE/1361509‑1361420

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.