New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2421927	149 (0.780)	35 (0.200)	18/146	NT	20.0%	intergenic (+43/+49)	USA300HOU_RS12475/hpxO	Putative 2‑hydroxyacid dehydrogenase/FAD‑dependent urate hydroxylase
	?	USA300TCH1516_ALE	= 2421954	145 (0.840)					intergenic (+70/+22)	USA300HOU_RS12475/hpxO	Putative 2‑hydroxyacid dehydrogenase/FAD‑dependent urate hydroxylase

AATGCTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2421831‑2421927 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacccccGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  <  USA300TCH1516_ALE/2421954‑2421865                                                                                                                                                                                             AATGCTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGA                                                                                                  >  1:1964136/1‑91  ATGCTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAA                                                                                                 >  1:2612918/1‑91   TGCTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAAC                                                                                                <  2:2376297/91‑1   TGCTGCAATTAGTGCAGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAAC                                                                                                <  2:3113341/91‑1    GCTGCAATTAGTGCCGTTCAAGGTAAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACC                                                                                               <  2:75123/91‑1     ctaCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCC                                                                                              <  2:1311159/88‑1     CTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAACCAAGAACCC                                                                                              >  2:513302/1‑91     CTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCC                                                                                              <  1:2118599/91‑1     CTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCC                                                                                              >  2:1011394/1‑91       GCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCC                                                                                            >  2:3747849/1‑91       GCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCC                                                                                            >  1:2761007/1‑91          ATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTA                                                                                         >  2:3717864/1‑91            TAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATG                                                                                       <  1:2535768/91‑1            TAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATG                                                                                       <  1:1462203/91‑1                        AGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAG                                                                           >  1:1503872/1‑91                          GTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCT                                                                         <  2:3876043/91‑1                           TGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTC                                                                        <  2:1144373/91‑1                           TGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCATATGTTGAAACGAGAGCTC                                                                        <  2:1964136/91‑1                             AGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAA                                                                      <  2:1379/91‑1                             AGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAA                                                                      <  1:638336/91‑1                              GAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCGGTATGTTGAAACGAGAGCTCAAC                                                                     <  2:1576160/91‑1                              GAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAAC                                                                     <  2:1576107/91‑1                               AAACCACAATTTGTCGTTAACTAATAATTGCATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACA                                                                    <  2:1877509/91‑1                               AAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACA                                                                    <  1:2835194/91‑1                               AAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACA                                                                    <  1:2836169/91‑1                                  CCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATAT                                                                 <  1:2299110/91‑1                                   ccCAATTTTTCGTTAACCAACAATTGAATCTATTATAATACCATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  2:2674589/89‑1                                   CACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  1:2727564/91‑1                                   CACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  1:3451164/91‑1                                   CACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  1:2266071/91‑1                                   CACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  2:2653923/91‑1                                   CACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  1:320017/91‑1                                   CACAATATGTCGTTAACTAATAAGTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATG                                                                <  2:1593564/91‑1                                    ACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGG                                                               <  2:2457709/91‑1                                     CAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGG                                                              <  1:1473658/91‑1                                      AATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGG                                                             <  2:1360946/91‑1                                       ATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGG                                                            <  2:1503872/91‑1                                       ATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGG                                                            <  2:165519/91‑1                                       ATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGG                                                            <  1:1920476/91‑1                                       ATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGG                                                            <  2:835886/91‑1                                       ATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGG                                                            <  2:825708/91‑1                                          TGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTC                                                         <  2:1025040/91‑1                                          TGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTC                                                         <  2:1549821/91‑1                                          TGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTC                                                         <  1:3655837/91‑1                                           GTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCT                                                        <  1:2210774/91‑1                                            TCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTT                                                       <  2:1973335/91‑1                                                  ACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTT                                                 <  1:1406803/91‑1                                                         ATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGT                                          <  2:1818625/91‑1                                                                            CATTATAAAGACAAGAACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATT                       <  1:3717864/91‑1                                                                                          aaaaCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACA         >  1:2690320/5‑91                                                                                          aaaaCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACA         >  1:2690489/5‑91                                                                                          aaaaCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACA         >  1:2690504/5‑91                                                                                           AACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTCTAATACATTCAATTATTAGTTAACGACAc        >  2:52689/1‑90                                                                                           AACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAA        <  2:1826554/91‑1                                                                                           AACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAA        >  2:1352510/1‑91                                                                                           AACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAA        >  2:168655/1‑91                                                                                           AACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAA        >  1:2575987/1‑91                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:849112/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:2806652/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:2826974/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:2826996/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:2827017/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       <  1:2827040/91‑1                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       >  1:2159649/1‑91                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       >  1:2160918/1‑91                                                                                            ACCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAA       >  1:2159661/1‑91                                                                                             CCCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAAT      <  2:1282189/91‑1                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     <  2:2030516/91‑1                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     >  1:2763690/1‑91                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     <  2:1023960/91‑1                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     <  2:1243728/91‑1                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     <  2:1243938/91‑1                                                                                              CCCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATT     <  2:1439597/91‑1                                                                                               CCCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTG    >  2:198128/1‑91                                                                                                CCGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGT   <  1:546784/91‑1                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  >  1:1324382/1‑91                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  >  1:3078215/1‑91                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  >  1:3405838/1‑91                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  >  1:3623486/1‑91                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  >  1:1324381/1‑91                                                                                                 CGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  <  2:1715980/91‑1                                                                                                                                                                                             AATGCTGCAATTAGTGCCGTTCAAGGTGAGAAACCACAATTTGTCGTTAACTAATAATTGAATTTATTATAATAACATTATAAAAACAAGAACCCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2421831‑2421927 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacccccGTATGTTGAAACGAGAGCTCAACATATGGGGGTTCTTGTTTTTATAATGTTATTATAATAAATTCAATTATTAGTTAACGACAAATTGTG  <  USA300TCH1516_ALE/2421954‑2421865

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