New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 940821	169 (0.890)	30 (0.170)	13/148	NT	17.5%	intergenic (+2/+54)	USA300HOU_RS04680/ptlE	Putative esterase/Neopentalenolactone D synthase
	?	USA300TCH1516_ALE	= 940872	126 (0.720)					intergenic (+53/+3)	USA300HOU_RS04680/ptlE	Putative esterase/Neopentalenolactone D synthase

GTCGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/940726‑940821 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ataaaaAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCATA  <  USA300TCH1516_ALE/940872‑940783                                                                                                                                                                                            GTCGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAA                                                                                                 <  2:2372867/91‑1 GTCGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAA                                                                                                 <  2:1842574/91‑1 GTCGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAA                                                                                                 >  1:491408/1‑91   CGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATA                                                                                               >  2:1557895/1‑91   CGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATA                                                                                               <  1:3761154/91‑1    GACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAA                                                                                              >  2:3207027/1‑91    GACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAA                                                                                              <  2:1194789/91‑1      CACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAA                                                                                            >  1:1368561/1‑91      CACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAA                                                                                            <  2:1025337/91‑1      CACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAA                                                                                            <  1:2577626/91‑1                           TTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATG                                                                       <  1:1930662/91‑1                                    ACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCA                                                              <  1:781591/91‑1                                             AATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTC                                                     <  1:3756859/91‑1                                              ATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCA                                                    <  1:1294660/91‑1                                               TTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAG                                                   <  1:1398868/91‑1                                               TTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAG                                                   <  2:594176/91‑1                                                TAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGC                                                  <  1:1114861/91‑1                                                      CAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAG                                            <  2:1033100/91‑1                                                       AGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGT                                           <  2:3492345/91‑1                                                        GTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTT                                          <  1:2949539/91‑1                                                        GTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTT                                          <  2:473278/91‑1                                                        GTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTT                                          <  2:2878341/91‑1                                                        GTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTT                                          <  2:473042/91‑1                                                            TGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTT                                      <  2:2175193/91‑1                                                            TGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTT                                      <  1:1743219/91‑1                                                            TGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTT                                      <  1:1743168/91‑1                                                            TGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTT                                      <  1:1743117/91‑1                                                             GCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTT                                     <  1:2273750/91‑1                                                             GCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTT                                     <  1:1718052/91‑1                                                             GCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTT                                     <  2:3558574/91‑1                                                             GCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTT                                     <  1:3829043/91‑1                                                              CGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAGAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTA                                    <  1:2077730/91‑1                                                              CGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTA                                    <  1:757217/91‑1                                                              CGTGGTACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTA                                    <  2:1934082/91‑1                                                                   TACAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTA                               <  2:888663/91‑1                                                                     CAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAA                             <  2:545404/91‑1                                                                     CAGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAA                             <  2:545369/91‑1                                                                      AGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAG                            <  1:699932/91‑1                                                                      AGTTGCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAG                            <  1:699908/91‑1                                                                          GCTATTAAACCTTTAAAATAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTT                        <  1:3151756/91‑1                                                                                            TAAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACG      >  1:1538617/1‑91                                                                                             AAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGC     <  2:1594488/91‑1                                                                                             AAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGC     <  1:1308914/91‑1                                                                                             AAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGC     <  2:1592596/91‑1                                                                                             AAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGC     >  2:3073126/1‑91                                                                                             AAAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGC     <  1:1308951/91‑1                                                                                              AAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCA    <  1:2258594/91‑1                                                                                              AAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCA    <  1:2258459/91‑1                                                                                              AAAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCA    <  2:3699410/91‑1                                                                                               AAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCAT   >  2:784062/1‑91                                                                                               AAAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCAT   >  2:1232679/1‑91                                                                                                AAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCATA  >  2:3592509/1‑91                                                                                                                                                                                            GTCGACACATGTATGGGATATAAAAATTAAGAATGACAAAGAACAATTAATTACAGTTATGCGTGGTACAGTTGCTATTAAACCTTTAAAATAAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/940726‑940821 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ataaaaAAACTGCTAGCCGTAGTTATGAATATCTCATAACATTTCAGCTAGCAGTTCTTTTATTTTAAAGGTTTAATAGCAACTGTACCACGCATA  <  USA300TCH1516_ALE/940872‑940783

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