New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 425019	196 (0.960)	13 (0.070)	10/146	NT	6.8%	intergenic (+34/‑392)	USA300HOU_RS01985/gpmA_1	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase
	?	USA300TCH1516_ALE	= 425031	176 (0.950)					intergenic (+46/‑380)	USA300HOU_RS01985/gpmA_1	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase

TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/424923‑425019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagatgACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  <  USA300TCH1516_ALE/425031‑424942                                                                                                                                                                                             TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATA                                                                                                  >  1:680853/1‑91  TAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAA                                                                                                 >  1:2291215/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:1905677/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:1905833/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  2:1589085/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               <  1:2787963/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               <  2:803029/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:530056/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:3331920/1‑91     TTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGA                                                                                              >  2:2515637/1‑91     TTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGA                                                                                              >  2:3349617/1‑91     TTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGA                                                                                              >  1:3627500/1‑91      TGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGAT                                                                                             <  2:3492273/91‑1      TGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGAT                                                                                             >  2:410867/1‑91      TGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGAT                                                                                             <  2:809198/91‑1      TGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGAT                                                                                             >  2:1624482/1‑91      TGGTTCAATTATCTTAATTGAAATCATAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGAT                                                                                             <  2:809790/91‑1       GGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG                                                                                            >  1:3464163/1‑91                ATCTTAATTGCAATCGTAATGTTTATTTTAAGATTTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAA                                                                                   <  2:3761585/91‑1                ATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAA                                                                                   <  2:2531666/91‑1                ATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAA                                                                                   <  1:1065728/91‑1                    TAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCC                                                                               <  1:2702224/91‑1                      ATTGCGATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCAT                                                                             <  2:3210635/91‑1                       TTGCAATCGTAACGTTAATTTTAAGAACTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATC                                                                            <  2:1424020/91‑1                        TGCAATCGTAAGGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCT                                                                           <  2:1647795/91‑1                        TGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCT                                                                           <  1:3145308/91‑1                         GCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTT                                                                          <  2:2165344/91‑1                             gCGTAAAGTTAAGTTTAAGAGATATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATT                                                                      <  2:1158729/90‑1                              CGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTT                                                                     <  2:300990/91‑1                               GTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTC                                                                    <  1:3127799/91‑1                                TAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTCA                                                                   <  2:1626727/91‑1                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTTTTTTTTTCTCATAGCTCTTAAAATTAACGTTACGATTG        >  2:917009/1‑91                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTt        >  2:407695/1‑90                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATACCTCTTAAAATTAACGTTACGATTc        >  2:1681171/1‑90                                                                                             AGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCA      >  2:599221/1‑91                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATATCTCTTAAAATTAACGTTACGATTGCAAT    >  2:226539/1‑91                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAAT    <  1:3471105/91‑1                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAAT    <  2:513372/91‑1                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAAT    <  2:74001/91‑1                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAAT    >  1:3078374/1‑91                                                                                               ATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAAT    <  2:274144/91‑1                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  2:3323688/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   <  1:3079682/91‑1                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  1:3278501/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  1:939598/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  <  2:892858/91‑1                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  2:999083/1‑91                                                                                                                                                                                             TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/424923‑425019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagatgACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  <  USA300TCH1516_ALE/425031‑424942

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.