New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2537764	149 (0.780)	22 (0.130)	14/138	NT	13.0%	intergenic (+118/+36)	USA300TCH1516_02423/gpmA_2	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase
	?	USA300TCH1516_ALE	= 2537785	166 (1.010)					intergenic (+139/+15)	USA300TCH1516_02423/gpmA_2	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase

TATTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2537664‑2537764 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagctgcatGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGCTA  <  USA300TCH1516_ALE/2537785‑2537697                                                                                                                                                                                                TATTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTA                                                                                                     >  2:2306187/1‑91 TATTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTA                                                                                                     <  1:2640013/91‑1   TTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAG                                                                                                   <  1:3384786/91‑1   TTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAG                                                                                                   <  2:885707/91‑1   TTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACACTATACTTAACTATTTCCTTACATTACTTCACATATTTAAG                                                                                                   <  2:2948416/91‑1     GTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAG                                                                                                 <  1:1743719/91‑1     GTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAG                                                                                                 <  1:3286715/91‑1     GTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAG                                                                                                 <  2:2984206/91‑1     GTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAG                                                                                                 >  1:687354/1‑91     GTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAG                                                                                                 <  2:2984221/91‑1      TATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGC                                                                                                >  2:2433443/1‑91      TATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGC                                                                                                >  1:1727469/1‑91      TATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGC                                                                                                <  2:2384413/91‑1        TGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTG                                                                                              >  2:657208/1‑91          TCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCA                                                                                            <  2:2767910/91‑1          TCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCA                                                                                            <  2:2767867/91‑1          TCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCA                                                                                            <  1:807418/91‑1           CTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCAT                                                                                           <  2:1440043/91‑1           CTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCAT                                                                                           >  1:3726322/1‑91                  TATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAG                                                                                                   <  2:981566/76‑1                  TATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAG                                                                                                   >  1:981566/1‑76                     TTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGG                                                                                 <  2:97034/91‑1                       TCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAG                                                                               >  2:163086/1‑91                             ATCCCTAGCTCGTTAATATAACCTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTG                                                                         <  1:1130816/91‑1                              TCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGT                                                                        <  1:3534634/91‑1                                CCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTAT                                                                      <  2:1727469/91‑1                                CCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTAT                                                                      <  2:2478664/91‑1                                CCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTAT                                                                      <  2:2727791/91‑1                                CCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACAAATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTAT                                                                      <  2:889366/91‑1                                CCTAGCTCGTTAATATAAACTCTATACTTAACTATTCCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTAT                                                                      <  2:3507166/91‑1                                 CTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATA                                                                     <  2:1237118/91‑1                                 CTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATA                                                                     <  2:1236290/91‑1                                 CTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATA                                                                     <  1:1495555/91‑1                                  TAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATAT                                                                    <  1:1174255/91‑1                                  TAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATAT                                                                    <  1:2745766/91‑1                                  TAGCTCGTTAATATAAACTCTATACTTAACTATTTCATTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATAT                                                                    <  2:3051983/91‑1                                   AGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATG                                                                   <  2:1920102/91‑1                                      TCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAG                                                                <  1:3379458/91‑1                                        GTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCAGATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCT                                                              <  1:3090947/91‑1                                          TAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCT                                                            <  1:2852486/91‑1                                             TATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAA                                                         <  1:3299268/91‑1                                                             AACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGT                                         <  1:163086/91‑1                                                                                TTCACATATTTAAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCGCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATA                      <  1:2139617/91‑1                                                                                           AAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGCGTTTATATT           >  1:3722596/1‑91                                                                                           AAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATT           >  2:159588/1‑91                                                                                           AAGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATT           >  1:2498252/1‑91                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTTAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTA          <  2:3198430/91‑1                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATCGAGTTTATATTA          <  1:3004608/91‑1                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTA          <  1:3787233/91‑1                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTA          <  2:2371024/91‑1                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTA          <  1:544160/91‑1                                                                                            AGAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTA          <  1:2615618/91‑1                                                                                             GAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAA         >  1:529984/1‑91                                                                                             GAGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAA         <  2:3152771/91‑1                                                                                              AGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAAC        <  1:2834895/91‑1                                                                                              AGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAAC        <  1:493292/91‑1                                                                                              AGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAAC        >  1:2453098/1‑91                                                                                              AGCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAAC        >  2:354595/1‑91                                                                                               GCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACG       >  1:2448590/1‑91                                                                                               GCTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACG       <  2:2679222/91‑1                                                                                                CTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA      >  2:2722764/1‑91                                                                                                CTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA      >  1:850785/1‑91                                                                                                CTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA      >  2:1135233/1‑91                                                                                                CTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA      >  2:1039887/1‑91                                                                                                CTGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA      >  2:967417/1‑91                                                                                                 TGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAG     >  1:2878039/1‑91                                                                                                 TGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAG     >  1:31714/1‑91                                                                                                 TGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAG     <  2:2337997/91‑1                                                                                                 TGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAG     <  1:97556/91‑1                                                                                                 TGCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAAAATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAG     >  1:346645/1‑91                                                                                                  GCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGC    >  2:3331997/1‑91                                                                                                  GCATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGC    >  1:2598489/1‑91                                                                                                   CATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGCT   >  1:946161/1‑91                                                                                                   CATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGCT   >  1:945844/1‑91                                                                                                    ATGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGCTA  <  2:3114571/91‑1                                                                                                                                                                                                TATTGTATGTCTAACTATATTTTCGAGTATCCCTAGCTCGTTAATATAAACTCTATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2537664‑2537764 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagctgcatGTACACAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGAGCTA  <  USA300TCH1516_ALE/2537785‑2537697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.