New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2537754 =	96 (0.980)	10 (0.120)	8/138	NT	12.1%	intergenic (+108/+46)	USA300TCH1516_02423/gpmA_2	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase
	?	USA300TCH1516_ALE	2537797 =	62 (0.730)					intergenic (+151/+3)	USA300TCH1516_02423/gpmA_2	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase

CTTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2537853‑2537754 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgcagctcttTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGAT  >  USA300TCH1516_ALE/2537797‑2537886                                                                                                                                                                                                CTTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATAT                                                                                                     <  1:521783/91‑1  TTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATG                                                                                                    >  1:1998202/1‑91  TTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATG                                                                                                    >  1:2207750/1‑91  TTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATG                                                                                                    >  1:1428567/1‑91   TGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGC                                                                                                   <  1:3583306/91‑1   TGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGC                                                                                                   <  1:3583083/91‑1   TGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGC                                                                                                   <  1:2333618/91‑1   TGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGC                                                                                                   <  1:2982644/91‑1   TGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGC                                                                                                   <  1:2982419/91‑1    GTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCA                                                                                                  >  1:2035242/1‑91        ATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTC                                                                                              >  1:2524832/1‑91        ATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTC                                                                                              >  1:2523824/1‑91         TGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCT                                                                                             >  1:2737326/1‑91         TGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCT                                                                                             >  1:3090581/1‑91          GAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT                                                                                            <  1:508563/91‑1          GAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT                                                                                            <  1:2536392/91‑1          GAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT                                                                                            <  1:2536660/91‑1          GAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT                                                                                            <  1:2536730/91‑1                                 TATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTA                                                                     >  1:1921868/1‑91                                                          AAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTC                                            >  1:2714362/1‑91                                                           AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCA                                           >  1:2213944/1‑91                                                                 GCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACA                                     >  1:1732947/1‑91                                                                  CATGTACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAA                                    >  1:2836781/1‑91                                                                       ACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGT                               >  1:3344378/1‑91                                                                       ACACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGT                               >  1:450050/1‑91                                                                        CACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTCTCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTG                              >  1:4151459/1‑91                                                                        CACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTG                              >  1:951095/1‑91                                                                         ACAAGGAGTGAGTGTATATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGC                             >  1:3814260/1‑91                                                                                        ccgTGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTC              <  1:178644/88‑1                                                                                          ATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTatga            <  1:1847548/91‑5                                                                                          ATGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCAT            >  1:57906/1‑91                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:1186264/91‑1                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:1240208/91‑1                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:1240209/91‑1                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:1240257/91‑1                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:1240679/91‑1                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           >  1:4037527/1‑91                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           >  1:3884756/1‑91                                                                                           TGCAGCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATA           <  1:3815635/91‑1                                                                                               GCTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTA       >  1:944002/1‑91                                                                                                CTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAA      >  1:4034465/1‑91                                                                                                CTCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAA      >  1:1814820/1‑91                                                                                                 TCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAAT     >  1:315722/1‑91                                                                                                 TCTTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAAT     <  1:2656826/91‑1                                                                                                   TTTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGA   <  1:1666065/91‑1                                                                                                   TTTTTTTATAAGAAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGA   >  1:3175657/1‑91                                                                                                   TTTGTTTATTAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGA   <  1:3731117/91‑1                                                                                                    TTTTTTATAAGTAGTATTTATCAATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGAT  >  1:1731908/1‑91                                                                                                                                                                                                CTTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2537853‑2537754 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgcagctcttTTTTTATAAGTAGTATTTATCTATAACTTCTAAATCATCCGTTAATTCATAAACAAGCGGTGCACCTGTTTTAATTTCATAATTAATGAT  >  USA300TCH1516_ALE/2537797‑2537886

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.