New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1627039	173 (0.850)	20 (0.110)	12/140	NT	10.9%	intergenic (‑192/+27)	USA300HOU_RS08070/gnd	hypothetical protein/6‑phosphogluconate dehydrogenase, decarboxylating
	?	USA300TCH1516_ALE	= 1627047	176 (0.990)					intergenic (‑200/+19)	USA300HOU_RS08070/gnd	hypothetical protein/6‑phosphogluconate dehydrogenase, decarboxylating

CTTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1626940‑1627039 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggatagtTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  USA300TCH1516_ALE/1627047‑1626958                                                                                                                                                                                                ctgTTAAGGTCAAGGATAATACTTGTGTAATTTTTTAGAGGTTGTGGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAA                                                                                                     <  2:966978/88‑1 CTTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAA                                                                                                     >  1:3250592/1‑91 CTTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAA                                                                                                     >  1:3250636/1‑91 CTTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAA                                                                                                     >  1:3250870/1‑91  TTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAA                                                                                                    >  1:901510/1‑91  TTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAA                                                                                                    >  1:3359344/1‑91    TTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAG                                                                                                  <  2:1814439/91‑1    TTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAG                                                                                                  <  2:1135556/91‑1      AAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGA                                                                                                <  1:1882298/91‑1      AAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATAAAAAAAAGGA                                                                                                <  2:2974804/91‑1       AGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGAT                                                                                               <  2:1259327/91‑1        GGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATA                                                                                              <  1:1479944/91‑1         GTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAG                                                                                             <  1:1318905/91‑1          cCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATAAAAAAAAATAAAAAAGGATAGT                                                                                            <  2:3916040/90‑1          TCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTTGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT                                                                                            <  2:3915250/91‑1          TCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT                                                                                            <  1:1610745/91‑1          TCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT                                                                                            <  2:1032975/91‑1          TCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT                                                                                            <  1:93028/91‑1          TCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTATATATTTATCAAAAGATATAAAAAAGGATAGT                                                                                            <  2:3881599/91‑1                  AATTCTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGAT                                                                                    <  1:3562148/91‑1                  AATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGAT                                                                                    <  1:3564004/91‑1                    TACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATAC                                                                                  <  2:3534758/91‑1                     ACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACT                                                                                 <  1:3491984/91‑1                     ACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACT                                                                                 <  1:1565486/91‑1                      CTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTA                                                                                <  1:1226067/91‑1                       TTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACTCTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTAT                                                                               <  1:1696770/91‑1                        TGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATC                                                                              <  1:2353185/91‑1                           GTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTT                                                                           <  2:655139/91‑1                           GTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTT                                                                           <  1:174612/91‑1                            TAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTT                                                                          <  1:2008746/91‑1                              ATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTT                                                                        <  2:265943/91‑1                              ATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTT                                                                        <  1:1047349/91‑1                              ATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTAGCCTTTTT                                                                        <  2:637015/91‑1                              ATTTGTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTT                                                                        <  1:3295598/91‑1                               TTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTTT                                                                       <  1:850584/91‑1                               TTTTTTATAGGTTGTAGCTACTCTAGCACACTCTCTGTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTTT                                                                       <  2:1579767/91‑1                                TTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTTTA                                                                      <  1:2304710/91‑1                                TTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTTTA                                                                      <  1:1328508/91‑1                                                              TCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTG                                        <  1:1778866/91‑1                                                                                           AAAGGATAGTTGAAAGATACTATCCTTTTTTTTATTTTTTGTTAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTt           >  2:2505993/1‑90                                                                                            AAGGATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTAC          >  1:2201554/1‑91                                                                                            AAGGATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGGGATAGAGTAGCTACAACCTATAAAAAATTAC          >  1:564915/1‑91                                                                                             AGGATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACA         <  2:704883/91‑1                                                                                               GATAGTTGAGAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACA       <  1:3785433/91‑1                                                                                                ATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAA      <  2:2470085/91‑1                                                                                                ATAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAA      <  1:1013394/91‑1                                                                                                 TAGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAG     >  2:3944344/1‑91                                                                                                  AGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  2:1044025/91‑1                                                                                                  AGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  1:2371477/91‑1                                                                                                  AGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  2:288451/91‑1                                                                                                  AGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  2:1044038/91‑1                                                                                                  AGTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  1:3412749/91‑1                                                                                                  AGTTGAAAGATACTATCCTGTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGT    <  2:288480/91‑1                                                                                                   GTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGTGTAGCTACAACCTATAAAAAATTACACAAGTA   >  1:3378030/1‑91                                                                                                   GTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTA   <  2:989115/91‑1                                                                                                   GTTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTA   >  1:1411417/1‑91                                                                                                   GTTGAAAGATACTATCCTTTTTTATATCTGTGGATAAATATAAATGAGAGTGTGATACAGTAGCTACAACCTATAAAAAATTACACAAGTA   <  1:3163408/91‑1                                                                                                   GTTGAAAGATACTATCCTTTTTTATATCTCTCGATAAATATAAACGAGAGTGTTATAGAGTAGCTACAACCTATAAAAAATTACACAAGTA   <  1:3162821/91‑1                                                                                                    TTGAAAGATACTATCCTTTTTTTTTTTTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  >  2:2586750/1‑91                                                                                                    TTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  1:538030/91‑1                                                                                                    TTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  1:3096737/91‑1                                                                                                    TTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  2:2761785/91‑1                                                                                                    TTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  1:594517/91‑1                                                                                                                                                                                                CTTTTAAGGTCAAGGATAATACTTGTGTAATTTTTTATAGGTTGTAGCTACTCTATCACACTCTCTTTTATATTTATCAAAAGATATAAAAAAGGATAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1626940‑1627039 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggatagtTGAAAGATACTATCCTTTTTTATATCTTTTGATAAATATAAAAGAGAGTGTGATAGAGTAGCTACAACCTATAAAAAATTACACAAGTAT  <  USA300TCH1516_ALE/1627047‑1626958

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.