New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2248208 =	88 (0.890)	4 (0.040)	4/150	NT	5.0%	intergenic (+2/+128)	coaW/USA300HOU_RS11505	Type II pantothenate kinase/hypothetical protein
	?	USA300TCH1516_ALE	2248263 =	68 (0.740)					intergenic (+57/+73)	coaW/USA300HOU_RS11505	Type II pantothenate kinase/hypothetical protein

AATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2248302‑2248208 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCAT  >  USA300TCH1516_ALE/2248263‑2248352                                                                                                                                                                                           AATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTC                                                                                                <  1:2624316/91‑1  ATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCT                                                                                               <  1:2654753/91‑1  ATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCT                                                                                               >  1:3798866/1‑91    GGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTT                                                                                             >  1:3775260/1‑91                                         AAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTC                                                        >  1:2890277/1‑91                                          AAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCC                                                       >  1:300288/1‑91                                                     ATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCA                                            >  1:2393618/1‑91                                                        TAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTTATTTTATGGTCTAAGTGTATTGAATACGTATTGCTCCATTTATTATCACTT                                         >  1:3549493/1‑91                                                                                           CTTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGT      >  1:772891/1‑91                                                                                            TTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTT     >  1:2358743/1‑91                                                                                            TTTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTT     >  1:3899208/1‑91                                                                                             TTTATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTC    >  1:3101476/1‑91                                                                                               TATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCAT  >  1:1037696/1‑91                                                                                                                                                                                           AATGGAACAATACGTATTCAAAACACTTAGACCATAAAATAAAAGGCCATTTATATAGCGTTTATTTAAAACAACGCGCATATAAATGGTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2248302‑2248208 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttATTTTATGGTCTAAGTGTTTTGAATACGTATTGTTCCATTTATTATCACTTAATTACTTACAACTCAATTCAATTAAAATGTAAGTTCAT  >  USA300TCH1516_ALE/2248263‑2248352

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