New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1355723	90 (0.920)	6 (0.070)	5/138	NT	7.3%	intergenic (+13/+41)	USA300HOU_RS06740/yclM	hypothetical protein/Aspartokinase 3
	?	USA300TCH1516_ALE	= 1355749	74 (0.870)					intergenic (+39/+15)	USA300HOU_RS06740/yclM	hypothetical protein/Aspartokinase 3

TTAAGCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1355624‑1355723 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagcaattcGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACCTAC  <  USA300TCH1516_ALE/1355749‑1355660                                                                                                                                                                                                TTAAGCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAA                                                                                                     <  1:158455/91‑1  TAAGCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAA                                                                                                    <  1:1185119/91‑1   AAGCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAA                                                                                                   <  1:1074516/91‑1     GCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGC                                                                                                 >  1:4103918/1‑91     GCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGC                                                                                                 >  1:1368391/1‑91       TACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAA                                                                                               >  1:1899448/1‑91         CTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATT                                                                                             >  1:3510522/1‑91         CTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATT                                                                                             >  1:2220427/1‑91                           AAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAA                                                                           <  1:1490494/91‑1                           AAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAA                                                                           <  1:2314902/91‑1                                        GGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAACTGCGTTATGAAT                                                              <  1:856584/91‑1                                         GTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAACTGCGTTATGAATT                                                             <  1:24749/91‑1                                                ACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTT                                                      <  1:1066625/91‑1                                                         GGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTAT                                             <  1:2652836/91‑1                                                                                             AGCAATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCT         >  1:196564/1‑91                                                                                                AATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCAC      >  1:2532512/1‑91                                                                                                AATACGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTCGCTCAC      <  1:3221210/91‑1                                                                                                 ATTCGTACCACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACC     <  1:2075621/91‑1                                                                                                 ATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACC     >  1:3112445/1‑91                                                                                                 ATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACC     >  1:1429968/1‑91                                                                                                 ATTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACC     >  1:1028170/1‑91                                                                                                  TTCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACCT    >  1:491764/1‑91                                                                                                   TCGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACCTA   >  1:468947/1‑91                                                                                                    CGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACCTAC  <  1:1725015/91‑1                                                                                                                                                                                                TTAAGCTACTATCAATTTTTTATTTTAAAATTTGTAGTAGGTGAGCAACGTATTAAGGATGCAATCCAGAGAACAATAAATAATTAAGAAAAAGCAATTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1355624‑1355723 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagcaattcGTAACACATGTATTCAACTGCGTTATGAATTGCTTTTTCTTAATTATTTATTGTTCTCTGGATTGCATCCTTAATACGTTGCTCACCTAC  <  USA300TCH1516_ALE/1355749‑1355660

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