New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1893332	24 (0.240)	39 (0.420)	8/150	NT	63.4%	intergenic (‑193/+154)	USA300TCH1516_01750/ytpA	hypothetical protein/Phospholipase YtpA
	?	USA300TCH1516_ALE	1910766 =	NA (NA)					intergenic (+299/‑256)	crcB_2/USA300TCH1516_01771	Putative fluoride ion transporter CrcB/hypothetical protein

GTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1893238‑1893332 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtgcc‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  >  USA300TCH1516_ALE/1910766‑1910855                                                                                                                                                                                            GTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAG                                                                                                 <  1:2230238/91‑1 GTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAG                                                                                                 <  1:1631572/91‑1   TGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTG                                                                                               <  1:1118682/91‑1   TGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTG                                                                                               <  1:570575/91‑1   TGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTG                                                                                               <  1:570559/91‑1   TGGAAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTG                                                                                               <  1:1118872/91‑1     GGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC                                                                                             >  1:3356844/1‑91     GGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC                                                                                             >  1:1725826/1‑91                TTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTC                                                                                 <  1:1822040/91‑1                    TTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTC                                                                             <  1:4034836/91‑1                    TTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTC                                                                             <  1:2145866/91‑1                    TTTTTTAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTC                                                                             <  1:389472/91‑1                    TTTTTTAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTC                                                                             <  1:389159/91‑1                    TTTTTAAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTC                                                                             <  1:705531/91‑1                     TTTTTAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCT                                                                            <  1:2171163/91‑1                     TTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCT                                                                            <  1:1701663/91‑1                     TTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCT                                                                            <  1:554970/91‑1                      ttttAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTT                                                                           <  1:4114404/87‑1                      ttttAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTT                                                                           <  1:3579184/87‑1                      tttaAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTT                                                                           <  1:3694527/87‑1                      TTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTT                                                                           <  1:36546/91‑1                      TTTTAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTT                                                                           <  1:500506/91‑1                       ttttAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTC                                                                          <  1:2923015/87‑1                       ttttAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTC                                                                          <  1:272672/87‑1                       ttttAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTC                                                                          <  1:1254922/87‑1                       ttttAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTC                                                                          <  1:1254664/87‑1                       tttAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:3365676/88‑1                       tttAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:3977633/88‑1                       tttAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCTCAGCCTCGGTCTT                                                                           <  1:4026631/88‑1                       tttAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:2573755/88‑1                       ttaAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:2665859/88‑1                       TTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:3050050/91‑1                       TTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:107300/91‑1                       TTCAAAGTAATTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTC                                                                          <  1:3962875/91‑1                        tttAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTCG                                                                         <  1:2576466/88‑1                        TCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCt                                                                         <  1:1727144/91‑2                        TCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCG                                                                         <  1:1727014/91‑1                        TCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCG                                                                         <  1:1726940/91‑1                         tAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGA                                                                        <  1:323187/90‑1                          AAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGAC                                                                       <  1:2210980/91‑1                           AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACT                                                                      <  1:927387/91‑1                           AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACT                                                                      <  1:3329950/91‑1                            AGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACTG                                                                     <  1:1307841/91‑1                             GTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACTGG                                                                    <  1:2142691/91‑1                                  tcAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTG                                                               <  1:3993949/89‑1                                                    TTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTTGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGC                                             <  1:2776871/91‑1                                                                 TTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACG                                <  1:2360774/91‑1                                                                                           GTGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACA      >  1:2856299/1‑91                                                                                           GTGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACA      <  1:507740/91‑1                                                                                           GTGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACA      <  1:504606/91‑1                                                                                            TGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTCCAT     >  1:3206507/1‑91                                                                                            TGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACAT     <  1:2720797/91‑1                                                                                            TGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACAT     >  1:3440528/1‑91                                                                                            TGCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACAT     >  1:545606/1‑91                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    >  1:1156403/1‑91                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    <  1:3898408/91‑1                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    >  1:2771871/1‑91                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    >  1:1157098/1‑91                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    >  1:1157193/1‑91                                                                                             GCC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATA    >  1:1576717/1‑91                                                                                              CC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATAC   >  1:36108/1‑91                                                                                              CC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATAC   <  1:1690013/91‑1                                                                                              CC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATAC   <  1:1689480/91‑1                                                                                              CC‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATAC   <  1:337060/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGCGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  >  1:3520927/1‑91                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:1262553/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:1778232/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:588786/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:1784683/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:724862/91‑1                                                                                               C‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  <  1:2294558/91‑1                                                                                                                                                                                            GTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1893238‑1893332 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtgcc‑GTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACT  >  USA300TCH1516_ALE/1910766‑1910855

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.