New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1217693	92 (0.940)	5 (0.060)	5/128	NT	5.9%	intergenic (+22/‑415)	USA300HOU_RS06060/USA300HOU_RS06065	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1217729	87 (1.110)					intergenic (+58/‑379)	USA300HOU_RS06060/USA300HOU_RS06065	hypothetical protein/hypothetical protein

ATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1217588‑1217693 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagctatagtgtttGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATCCT  <  USA300TCH1516_ALE/1217729‑1217640                                                                                                                                                                                                      ATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAA                                                                                                           >  1:906665/1‑91  TAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAA                                                                                                          >  1:2612569/1‑91  TAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAA                                                                                                          >  1:1278382/1‑91  TAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAA                                                                                                          >  1:369152/1‑91  TAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAA                                                                                                          >  1:369274/1‑91  TAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAA                                                                                                          >  1:369499/1‑91   AAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAA                                                                                                         >  1:415946/1‑91   AAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAA                                                                                                         >  1:4086327/1‑91   AAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAA                                                                                                         >  1:3607034/1‑91     AAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAG                                                                                                       >  1:497568/1‑91     AAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAG                                                                                                       <  1:515914/91‑1      AAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGC                                                                                                      <  1:1141608/91‑1      AAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGC                                                                                                      <  1:1141735/91‑1         TAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTAT                                                                                                   <  1:2165300/91‑1          AAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATA                                                                                                  <  1:1947786/91‑1          AAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATA                                                                                                  >  1:1238973/1‑91           AAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAG                                                                                                 >  1:3799860/1‑91           AAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAG                                                                                                 <  1:1176881/91‑1           AAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAG                                                                                                 >  1:3799877/1‑91           AAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAG                                                                                                 >  1:1087114/1‑91           AAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAG                                                                                                 >  1:1087488/1‑91            AACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGT                                                                                                >  1:3746983/1‑91            AACAACTATAGATCATAATGATGATTTATGTCAACATGTAAAGGATATATTACATAATCAAGAACAAATTTAAAAACAAAAAAGCTATAGT                                                                                                <  1:3318538/91‑1             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:3920068/1‑91             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               <  1:3790465/91‑1             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:3920625/1‑91             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:3407210/1‑91             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:2233887/1‑91             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:1714568/1‑91             ACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTG                                                                                               >  1:1714542/1‑91               AACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTT                                                                                             >  1:2182261/1‑91               AACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTT                                                                                             <  1:1173801/91‑1                                                     AGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTA                                                       <  1:731758/91‑1                                                            ATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTA                                                <  1:534435/91‑1                                                             TTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTAT                                               <  1:653444/91‑1                                                               ACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAG                                             <  1:442106/91‑1                                                                CGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGC                                            <  1:2419844/91‑1                                                                                              AGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTAC              <  1:197322/91‑1                                                                                              AGCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTAC              <  1:197293/91‑1                                                                                               GCTATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACG             >  1:946621/1‑91                                                                                                 TATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTA           <  1:1773585/91‑1                                                                                                  ATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAA          >  1:3819163/1‑91                                                                                                  ATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAA          <  1:3138382/91‑1                                                                                                  ATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAA          <  1:1158913/91‑1                                                                                                  ATAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTGTGTTTTTAAATTTGTTCTTGTTTACGTAA          >  1:2060660/1‑91                                                                                                   TAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAAT         <  1:878792/91‑1                                                                                                   TAGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAAT         <  1:878849/91‑1                                                                                                    AGTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATA        >  1:2518565/1‑91                                                                                                     GTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATAT       >  1:332543/1‑91                                                                                                     GTGTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATAT       >  1:3016116/1‑91                                                                                                       GTTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATAT     >  1:1371163/1‑91                                                                                                        TTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATC    <  1:2795450/91‑1                                                                                                        TTTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATC    >  1:821197/1‑91                                                                                                         TTGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATCC   >  1:3521761/1‑91                                                                                                          TGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATCCT  <  1:478027/91‑1                                                                                                          TGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATCCT  <  1:2102857/91‑1                                                                                                                                                                                                      ATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1217588‑1217693 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagctatagtgtttGTAATATTCGGATGCGGTTAAGCAGCCCCTGATATTAAACACTATAGCTTTTTTGTTTTTAAATTTGTTCTTGTTTACGTAATATATCCT  <  USA300TCH1516_ALE/1217729‑1217640

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