New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	869579 =	220 (1.150)	25 (0.150)	16/140	NT	12.4%	intergenic (+1262/+60)	smpB/USA300HOU_RS04240	SsrA‑binding protein/hypothetical protein
	?	USA300TCH1516_ALE	869621 =	162 (0.970)					intergenic (+1304/+18)	smpB/USA300HOU_RS04240	SsrA‑binding protein/hypothetical protein

GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/869677‑869579 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttcatagctaATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  >  USA300TCH1516_ALE/869621‑869710                                                                                                                                                                                               GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTT                                                                                                    >  1:1850358/1‑91 GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTT                                                                                                    >  1:3415524/1‑91 GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTT                                                                                                    <  2:2046050/91‑1 GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTT                                                                                                    >  1:3415334/1‑91  AGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTC                                                                                                   <  1:1134725/91‑1  AGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTC                                                                                                   >  2:1744401/1‑91  AGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTC                                                                                                   >  1:1507277/1‑91    TTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCAT                                                                                                 <  2:2159748/91‑1    TTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCAT                                                                                                 <  2:2307326/91‑1    TTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCAT                                                                                                 <  2:2309050/91‑1    TTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCAT                                                                                                 <  1:3500128/91‑1    TTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCAT                                                                                                 <  1:3500159/91‑1     TATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATA                                                                                                >  2:3274630/1‑91     TATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATA                                                                                                <  2:1651025/91‑1      ATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAG                                                                                               <  1:2873010/91‑1       TATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGGAGGAATCTATGACGATAGATTTTTTCATAGC                                                                                              <  1:957141/91‑1       TATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGC                                                                                              <  1:2790336/91‑1        ATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCT                                                                                             <  1:3497038/91‑1        ATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCT                                                                                             <  1:1628066/91‑1         TGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTA                                                                                            <  1:1917523/91‑1         TGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTA                                                                                            >  1:2283921/1‑91         TGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTA                                                                                            <  1:280921/91‑1                TTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAAAAATCTATCGTCATAGATTCCTTCATAGCTAATCTTAG                                                                                     <  1:144403/91‑1                         AGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAG                                                                                               >  2:3527826/1‑72                         AGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAG                                                                                               <  1:3527826/72‑1                                       aagATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGAT                                                              >  1:2511430/4‑91                                       AAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGAT                                                              >  1:724788/1‑91                                        AAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATG                                                             >  1:2451727/1‑91                                           TAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTA                                                          >  1:1518355/1‑91                                            AAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTAT                                                         >  2:3885170/1‑91                                            AAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTAT                                                         >  2:2693336/1‑91                                             AACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATT                                                        >  2:680703/1‑91                                                ATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTACATTTTTATTCTAGGATACTATTTAT                                                     >  2:3366242/1‑91                                                  ACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCA                                                   >  1:2861922/1‑91                                                       GATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCA                                              >  2:3324904/1‑91                                                         TTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTTTTTTTTGTTGCTATTTATCAATTCAAC                                            >  2:3698197/1‑91                                                         TTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAAC                                            >  2:1046931/1‑91                                                          TAGCTATGAAGGCATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACA                                           >  1:2994049/1‑91                                                          TAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACA                                           >  1:2350739/1‑91                                                          TAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACA                                           >  1:2350363/1‑91                                                          TAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACA                                           >  2:1908534/1‑91                                                             CTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATAT                                        >  1:1350961/1‑91                                                             CTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATAT                                        >  1:421867/1‑91                                                             CTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATAT                                        >  1:1960601/1‑91                                                              TATGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATA                                       >  1:2681465/1‑91                                                                TGAAGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAAC                                     >  1:1621442/1‑91                                                                   AGGAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCA                                  >  1:2252788/1‑91                                                                     GAATCTATGACGATAGATTTTTTCATAGCTTATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACT                                >  2:3154933/1‑91                                                                     GAATCTATGACGATAGATTTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACT                                >  1:1168383/1‑91                                                                                       TTTTTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAA              >  2:2088676/1‑91                                                                                          TTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATAT           <  1:68670/91‑1                                                                                          TTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATAT           <  2:1197488/91‑1                                                                                          TTCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATAT           <  2:2308263/91‑1                                                                                           TCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATA          <  1:2565276/91‑1                                                                                           TCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATA          <  2:977496/91‑1                                                                                           TCATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATA          >  2:2066340/1‑91                                                                                            CATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATAT         >  1:1118979/1‑91                                                                                             ATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATC        <  2:1230589/91‑1                                                                                             ATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATC        >  2:849790/1‑91                                                                                             ATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATC        <  2:1230516/91‑1                                                                                             ATAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATC        >  1:3579327/1‑91                                                                                              TAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCA       <  1:1350617/91‑1                                                                                              TAGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCA       <  1:1350242/91‑1                                                                                               AGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCAT      <  1:2159748/91‑1                                                                                               AGCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCAT      <  2:3402110/91‑1                                                                                                GCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATT     <  1:1524929/91‑1                                                                                                GCTAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATT     <  1:1255671/91‑1                                                                                                  TAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAA   >  2:1199589/1‑91                                                                                                  TAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAA   >  1:3524936/1‑91                                                                                                  TAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAA   <  1:3523904/91‑1                                                                                                  TAATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAA   <  2:424753/91‑1                                                                                                  TAATCTTAGTACGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAA   <  1:3523855/91‑1                                                                                                   AATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  >  1:963410/1‑91                                                                                                   AATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  <  2:557437/91‑1                                                                                                   AATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  >  2:2333006/1‑91                                                                                                   AATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  >  2:1570350/1‑91                                                                                                                                                                                               GAGTTATATGTTGAGTTGATAAATAGCATCCTAAAATAAAAATAAACATACTAAGATTAGCTATGAAGGAATCTATGACGATAGATTTTTTCATAGCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/869677‑869579 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttcatagctaATCTTAGTATGTTTATTTTTATTTTAGGATGCTATTTATCAACTCAACATATAACTCACTATTTTTATAACCTTCTAATATATCATTAAC  >  USA300TCH1516_ALE/869621‑869710

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.