New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2248208 =	134 (1.080)	8 (0.070)	8/248	NT	6.0%	intergenic (+2/+128)	coaW/USA300HOU_RS11505	Type II pantothenate kinase/hypothetical protein
	?	USA300TCH1516_ALE	2248263 =	121 (1.010)					intergenic (+57/+73)	coaW/USA300HOU_RS11505	Type II pantothenate kinase/hypothetical protein

ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2248348‑2248208 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTTTAAA  >  USA300TCH1516_ALE/2248263‑2248402                                                                                                                                                                                                                                                                                           ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT                                                                                                                                              <  1:366615/141‑1 ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT                                                                                                                                              <  1:663144/141‑1 ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT                                                                                                                                              <  2:367914/141‑1 ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT                                                                                                                                              <  3:197415/141‑1       ATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTA                                                                                                                                        <  2:761794/141‑1                                                                                        AAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTT                                                       >  1:678442/1‑141                                                                                           GGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCAT                                                    >  2:821383/1‑141                                                                                               ATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGA                                                >  1:458997/1‑141                                                                                                 TTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACA                                              >  3:195725/1‑141                                                                                                  TATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAA                                             >  2:161032/1‑141                                                                                                   ATATAGCGGTTATTTAAAACAACGCTCATATAAATGGCCTGTTATTTTATGGTCTAAGGGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTATTTACAACGCAATTCAATTAAAATGTAAGTTCATGATACAAT                                            >  4:293523/1‑141                                                                                                    TATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATT                                           >  2:567019/1‑141                                                                                                                                         CTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTT      <  2:632140/141‑1                                                                                                                                          TTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTTT     <  1:816422/141‑1                                                                                                                                          TTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTTT     <  2:927870/141‑1                                                                                                                                             TATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTTTAAA  >  1:732304/1‑141                                                                                                                                                                                                                                                                                           ACTTACATTTTAATTGAATTGAGTTGTAAGTAATTAAGTGATAATAAATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2248348‑2248208 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCATTAGACAATTTTTGCGCTGAAACAATTGTACCAACCACGCCAGTTTTTAAA  >  USA300TCH1516_ALE/2248263‑2248402

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.