New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1138356	199 (0.980)	13 (0.070)	9/140	NT	6.8%	intergenic (‑121/+82)	isdB/isdA	Iron‑regulated surface determinant protein B/Iron‑regulated surface determinant protein A
	?	USA300TCH1516_ALE	= 1138378	181 (1.020)					intergenic (‑143/+60)	isdB/isdA	Iron‑regulated surface determinant protein B/Iron‑regulated surface determinant protein A

TGTATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1138257‑1138356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taacctatgtCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAATC  <  USA300TCH1516_ALE/1138378‑1138289                                                                                                                                                                                                TGTATATTATCAACTGATAATCATTATGAATTGATTACTTGTATTGTACTTTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAAT                                                                                                     <  2:3006168/91‑1 TGTATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAAT                                                                                                     <  2:3745972/91‑1  GTATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATA                                                                                                    >  1:1739471/1‑91  GTATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATA                                                                                                    >  2:1759167/1‑91   TATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAA                                                                                                   >  2:1322800/1‑91    ATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAAC                                                                                                  <  1:2981257/91‑1     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGTAACGTTATTTTATAAAAAAGTAACC                                                                                                 >  2:3655379/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  1:1218565/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  2:457251/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 <  2:2501093/91‑1     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  2:1667840/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  1:53093/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  1:401313/1‑91     TATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACC                                                                                                 >  1:29822/1‑91       TTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTA                                                                                               >  2:938239/1‑91       TTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTA                                                                                               >  2:650558/1‑91        TATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTAT                                                                                              >  1:1105063/1‑91        TATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTAT                                                                                              >  2:2928930/1‑91        TATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTAT                                                                                              <  2:1002697/91‑1        TATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTAT                                                                                              >  1:3739391/1‑91         ATCAACTGATAATCATTATCAATTGCTTCCTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATG                                                                                             >  1:2202212/1‑91         ATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATG                                                                                             <  1:1366862/91‑1         ATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATG                                                                                             <  1:2098560/91‑1         ATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATG                                                                                             >  2:3541370/1‑91          TCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGCAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGT                                                                                            >  2:3872526/1‑91          TCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGT                                                                                            >  2:2426298/1‑91          TCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGT                                                                                            >  2:2426865/1‑91                        TTATCAATTGATTACTTGTATTGTACAGTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCAT                                                                              <  2:1352310/91‑1                        TTATCAAGTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTTCAACGTTATATTAAAAAAAAATAACCTATGTCATAGATATTTCAT                                                                              <  2:1352239/91‑1                           TCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAAT                                                                           <  1:2026686/91‑1                             AATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCT                                                                         <  1:1409577/91‑1                                       TTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTGTAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGG                                                               <  1:3946789/91‑1                                       TTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGG                                                               <  2:1887797/91‑1                                       TTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGG                                                               <  1:177632/91‑1                                       TTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGG                                                               <  1:785389/91‑1                                        TGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGGT                                                              <  2:574482/91‑1                                        TGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGGT                                                              <  2:711907/91‑1                                         GTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGGTT                                                             <  2:1729339/91‑1                                           ATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGTCATAGATATTTCATAATCTATAACATAGGTTAT                                                           <  1:3590677/91‑1                                                 CATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAGCCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTT                                                     <  1:2907701/91‑1                                                                                           TAACCTATGTTATAGATTATGAAATATCTATGACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATA           >  1:2827017/1‑91                                                                                           TAACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATA           <  2:2346921/91‑1                                                                                           TAACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATA           >  1:2561942/1‑91                                                                                           TAACCTATGTCATAGATATTTCATAAGCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATA           <  2:2349410/91‑1                                                                                            AACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATAC          <  1:2515067/91‑1                                                                                            AACCTATGTCATAAATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATAC          <  2:56268/91‑1                                                                                             ACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACA         >  1:2346012/1‑91                                                                                             ACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACA         >  1:864716/1‑91                                                                                             ACCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACA         >  1:864664/1‑91                                                                                              CCTATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAA        <  2:2616817/91‑1                                                                                               aTATGTCATAGATATTTCATAATCTATAACATATGTGATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAG       <  2:3919926/90‑1                                                                                                TATGTGATAGATATTGCATAATCTATAACAGAGGTTATTTTTTTATAAAATAACGTTGGAATGAACTAACATTGCAATGTACAATAGAAGT      <  2:1016746/91‑1                                                                                                TATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGT      >  1:607335/1‑91                                                                                                 ATGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTA     >  2:3833710/1‑91                                                                                                  TGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAA    <  1:307528/91‑1                                                                                                  TGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAA    <  1:2776277/91‑1                                                                                                  TGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAA    <  1:2776123/91‑1                                                                                                  TGTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAA    <  1:3898095/91‑1                                                                                                   GTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAGAATAACGTTGCAATTAACTACCATTTCAATGTACAATACAAGTAAT   >  1:424599/1‑91                                                                                                   GTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAAT   <  2:3589962/91‑1                                                                                                   GTCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAAT   <  1:1405564/91‑1                                                                                                    TCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAATC  <  1:3850594/91‑1                                                                                                                                                                                                TGTATATTATCAACTGATAATCATTATCAATTGATTACTTGTATTGTACATTGAAATGTTAGTTAATTGCAACGTTATTTTATAAAAAAATAACCTATGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1138257‑1138356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taacctatgtCATAGATATTTCATAATCTATAACATAGGTTATTTTTTTATAAAATAACGTTGCAATTAACTAACATTTCAATGTACAATACAAGTAATC  <  USA300TCH1516_ALE/1138378‑1138289

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.