New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1660030	40 (0.870)	5 (0.120)	4/238	NT	11.7%	coding (1279/1464 nt)	gluP	Rhomboid protease GluP
	?	USA300TCH1516_ALE	= 1660054	39 (0.920)					coding (1255/1464 nt)	gluP	Rhomboid protease GluP

TTTTTCTAAGTTAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1659881‑1660030 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attctaagtccGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCATTAAATGATGATGAAAAAGCATTAAAATATGTGCGTAAAGCATTAAATG  <  USA300TCH1516_ALE/1660054‑1659919                                                                                                                                                                                                                                                                                                TTTTTCTAAGTTAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACAT                                                                                                                                                   <  2:264119/141‑1     TCTAAGTTAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTA                                                                                                                                               >  1:571303/1‑141     TCTAAGTTAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACACAGATATTTTAACGCTTTTTCATCTTCATTTAAGGAACGATTTGCTATCGCAAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTA                                                                                                                                               >  2:283664/1‑141                              TAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGACCGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGA                                                                                                                      <  2:164961/141‑1                                        ATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTT                                                                                                            <  1:356593/141‑1                                        ATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTT                                                                                                            <  1:361556/141‑1                                         TTTAATGCTTTACGCACAGATTTTAATGCTTTTTCATCATCATGTAATGAACTACGTGCGATCTGGAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTA                                                                                                           <  1:783594/141‑1                                             ATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAAT                                                                                                       <  1:117606/141‑1                                                                                                                                                  AGTCCGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGAAAATCGTTCATTAAATGATGATGAAAAAGCATTAAAATATGTGCGTAAAGCAGTAAATG  >  1:93967/1‑141                                                                                                                                                                                                                                                                                                TTTTTCTAAGTTAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1659881‑1660030 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attctaagtccGAAGGTATGACAGAATGGGAGCGAGGACTTAGAATGTTTCCTAAATCAGGTTTATTAAATTTTGAGTTAGCGATAGCAAATCGTTCATTAAATGATGATGAAAAAGCATTAAAATATGTGCGTAAAGCATTAAATG  <  USA300TCH1516_ALE/1660054‑1659919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.