New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 954375	107 (0.560)	9 (0.050)	6/138	NT	8.2%	intergenic (+29/+474)	gluD/glpQ_1	NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase
	?	USA300TCH1516_ALE	= 954395	109 (0.660)					intergenic (+49/+454)	gluD/glpQ_1	NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase

ATGAGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/954275‑954375 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttaacgagcttAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACGTT  <  USA300TCH1516_ALE/954395‑954306                                                                                                                                                                                                 ATGAGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATT                                                                                                      >  1:1141467/1‑91 ATGAGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATT                                                                                                      <  1:2521398/91‑1   GAGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTA                                                                                                    <  1:347615/91‑1    AGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAA                                                                                                   <  1:2066522/91‑1    AGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAA                                                                                                   <  1:1446994/91‑1    AGACGTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAA                                                                                                   <  2:939690/91‑1     GACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAAC                                                                                                  <  1:2052097/91‑1     GACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAAC                                                                                                  <  2:168670/91‑1      ACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACG                                                                                                 <  2:3640309/91‑1       CTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGA                                                                                                >  2:2931779/1‑91          GCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCT                                                                                             <  1:1434359/91‑1           CAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTT                                                                                            >  1:922506/1‑91           CAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTT                                                                                            >  1:1306863/1‑91           CAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTT                                                                                            >  2:1772785/1‑91                             TTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTC                                                                          <  2:649637/91‑1                              TAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCC                                                                         <  2:1125658/91‑1                                 ACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAA                                                                      <  1:1172664/91‑1                                  CGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAG                                                                     <  2:704873/91‑1                                  CGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAG                                                                     <  2:2039864/91‑1                                  CGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAG                                                                     <  1:2564774/91‑1                                   GTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGC                                                                    <  1:1479438/91‑1                                    TACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCT                                                                   <  1:595621/91‑1                                    TACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCT                                                                   <  1:3780560/91‑1                                                                                           TTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCT            <  2:1113473/91‑1                                                                                           TTAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCT            <  2:1112570/91‑1                                                                                            TAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTG           <  2:1633278/91‑1                                                                                            TAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTG           <  2:2953514/91‑1                                                                                            TAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTG           <  1:1000940/91‑1                                                                                            TAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTG           >  1:3371193/1‑91                                                                                            TAACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTG           <  1:2044875/91‑1                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          >  1:1601398/1‑91                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          <  1:1648123/91‑1                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          >  2:2299905/1‑91                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          <  1:2171455/91‑1                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          <  1:1280173/91‑1                                                                                             AACGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGC          <  1:2589225/91‑1                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        <  2:2769201/91‑1                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        >  1:352981/1‑91                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        >  2:694019/1‑91                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        <  2:1621175/91‑1                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        <  2:1908783/91‑1                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        <  2:129204/91‑1                                                                                               CGAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTG        <  2:129219/91‑1                                                                                                GAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGT       <  1:2115659/91‑1                                                                                                GAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGT       <  2:3390274/91‑1                                                                                                GAGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGT       <  1:972064/91‑1                                                                                                 AGCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTA      <  2:3621960/91‑1                                                                                                  GCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTAC     <  1:2886284/91‑1                                                                                                  GCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTAC     <  1:2887268/91‑1                                                                                                  GCTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTAC     <  1:2632930/91‑1                                                                                                   CTTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACG    <  2:210940/91‑1                                                                                                    TTATGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGAACGT   <  1:3061285/91‑1                                                                                                    TTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACGT   >  1:2037105/1‑91                                                                                                    TTAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACGT   <  1:1873852/91‑1                                                                                                     TAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACGTT  <  2:2151265/91‑1                                                                                                                                                                                                 ATGAGACTTGCAGCATATATCATAGGTATTAAACGTACAGCAGAAGCAGCTAGATATCGTGGTTGGGCATAATTAATTATCATATGTGATTTAACGAGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/954275‑954375 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttaacgagcttAGGGCTTTGTTTTCTGTCCCAAGCTCGTTAAATCACATATGATAATTAATTATGCCCAACCACGATATCTAGCTGCTTCTGCTGTACGTT  <  USA300TCH1516_ALE/954395‑954306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.