New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2257232 =	80 (0.780)	4 (0.040)	3/248	NT	5.2%	coding (293/414 nt)	USA300HOU_RS11555	hypothetical protein
	?	USA300TCH1516_ALE	2257282 =	71 (0.730)					coding (243/414 nt)	USA300HOU_RS11555	hypothetical protein

GCAAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2257377‑2257232 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taatttAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGCCGCTTCTGGATGTTGTTTAAAAAATTGTTGGCCAACTTC  >  USA300TCH1516_ALE/2257282‑2257416                                                                                                                                                                                                                                                                                           GCAAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGT                                                                                                                                              >  2:1144100/1‑141  CAAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAGCCAGTCCGTA                                                                                                                                             >  1:716/1‑141  CAAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTA                                                                                                                                             >  2:764565/1‑141   AAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCGTGTACCTATACCAGTCCGTAA                                                                                                                                            <  1:618476/141‑1     ATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATT                                                                                                                                          >  2:650073/1‑141                                                                                                TAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATTTAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTT                                               >  2:409864/1‑141                                                                                                      ATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATTTAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGC                                         >  1:172072/1‑141                                                                                                      ATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATTTAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGC                                         >  1:720284/1‑141                                                                                                                                 TAAACCAGTCCGTAATTTAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGCCGCTTCTGGATGTTGTTTAAAAAATTG              <  1:409864/141‑1                                                                                                                                             TAATTTAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGCCGCTTCTGGATGTTGTTTAAAAAATTGTTGGCCAACTTC  >  2:473523/1‑141                                                                                                                                                                                                                                                                                           GCAAATAAAAATAGTGTGATTTTACAGAAAGGTGATCGTATATATTTTGAATCGCAGGCGATTATTAAACTAATCACAGCACTACCTAATCGAACTAAATTATTGGGCGTAGGTTTATGGCTTGTACCTAAACCAGTCCGTAATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2257377‑2257232 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taatttAGTTCGATTAGGTAGTGCTGTGATTAGTTTAATAATCGCCTGCGATTCAAAATATATACGATCACCTTTCTGTAAAATCACACTATTTTTATTTGCCGCTTCTGGATGTTGTTTAAAAAATTGTTGGCCAACTTC  >  USA300TCH1516_ALE/2257282‑2257416

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.