New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	854380 =	116 (0.830)	7 (0.050)	6/246	NT	6.0%	intergenic (‑275/‑460)	USA300HOU_RS04170/zipA_1	Epimerase family protein/Cell division protein ZipA
	?	USA300TCH1516_ALE	854405 =	110 (0.830)					intergenic (‑300/‑435)	USA300HOU_RS04170/zipA_1	Epimerase family protein/Cell division protein ZipA

TTAAGTGTTGTGTTAAAAGTTTTTATGTTTAGATTGTTATATTACTATGTATTCTTAAATTTGTTTAAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAATAAAAACGACCCGCACGATTAACGTACGGGTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/854524‑854380 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgggtcGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTTTC  >  USA300TCH1516_ALE/854405‑854542                                                                                                                                                                                                                                                                                             TTAAGTGTTGTGTTAAAAGTTTTTATGTTTAGATTGTTATATTACTATGTATTCTTAAATTTGTTTAAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAATAAAAACGACCCGCACGATTAACGTACG                                                                                                                                                <  1:347776/141‑1   AAGTGTTGTGTTAAAAGTTTTTATGTTTAGATTGTTATATTACTATGTATTCTTAAATTTGTTTAAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAATAAAAACGACCCGCACGATTAACGTACGGG                                                                                                                                              >  1:208423/1‑141    AGTGTTGTGTTAAAAGTTTTTATGTTTAGATTGTTATATTACTATGTATTCTTAAATTTGTTTAAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAATAAAAACGACCCGCACGATTAACGTACGGGT                                                                                                                                             >  2:369796/1‑141                                                                   AAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAAGAAAAACGACGGGTACGTTAATCGTGCGGGTCGTTTTTATTTATTTATTATTACCAATATACATCAATTTAAAGCATTAATTTTTTAAACAAAa                                                                              >  2:713342/1‑140                                                                                                                             CGCACGATTAACGTACGGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATCAAAACTTTTAACACAACACTTAA                    >  1:610396/1‑141                                                                                                                             CGCACGATTAACGTACGGGTCGTTTTTATTTATTTCTTACTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAA                    >  2:1167561/1‑141                                                                                                                               CACGATTAACGTACGGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAA                                                                                                         >  1:857415/1‑54                                                                                                                               CACGATTAACGTACGGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAA                                                                                                         <  2:857415/54‑1                                                                                                                                ACGATTAACGTACGGGTCGTTTTTATTTATTTCTTATTCCCATTATACAGCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACC                 >  2:85291/1‑141                                                                                                                                  GATTAACGTACGGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAA               >  1:753789/1‑141                                                                                                                                            CGGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATT     >  3:301583/1‑141                                                                                                                                             GGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTT    <  2:848712/141‑1                                                                                                                                             GGGTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTT    >  4:164458/1‑141                                                                                                                                               GTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTTTC  <  2:347776/141‑1                                                                                                                                               GTCGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTTTC  <  3:362410/141‑1                                                                                                                                                                                                                                                                                             TTAAGTGTTGTGTTAAAAGTTTTTATGTTTAGATTGTTATATTACTATGTATTCTTAAATTTGTTTAAAAAATTAATGCTTTAAATTGATGTATAATGGGAATAAGAAATAAATAAAAACGACCCGCACGATTAACGTACGGGTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/854524‑854380 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgggtcGTTTTTATTTATTTCTTATTCCCATTATACATCAATTTAAAGCATTAATTTTTTAAACAAATTTAAGAATACATAGTAATATAACAATCTAAACATAAAAACTTTTAACACAACACTTAAACCAATGCTTTAATTTTC  >  USA300TCH1516_ALE/854405‑854542

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