New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	20 (1.080)	15 (0.910)	13/228	0.3	52.8%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	9 (0.550)					coding (1/825 nt)	hlb_2	Phospholipase C

TTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2085436‑2085296 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAAT  <  USA300TCH1516_ALE/2128343‑2128216                                                                                                                                                                                                                                                                                TTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATCAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                              >  2:203728/1‑129            AAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATAC                                                                                                                                   <  1:199435/129‑1              AAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACAT                                                                                                                                 <  2:211888/129‑1                  TCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAGACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAA                                                                                                                             >  1:118172/1‑129                        agATTTTATTTTATATGAGGTATTATTGAGAATGATAAAGTTATAAAGCTTGATATTA‑TGGTGTTTTACTTTTGGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTG                                                                                                                       <  2:9080/127‑1                           TTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAA                                                                                                                    >  2:91027/1‑129                                         AGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATT                                                                                                      <  1:189658/129‑1                                         AGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATT                                                                                                      <  2:199464/129‑1                                         AGGTATTATTAATAATGATAAAGTTATAAACCTTGATCTTAGTTCT‑TTGTATTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATT                                                                                                      <  2:166500/129‑1                                              TTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGATAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTT                                                                                                 >  1:134678/1‑129                                                 TTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATTATAAGTAATTTTATGTTAAAAGTCTTCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGG                                                                                              <  1:94068/129‑1                                                        TGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTTAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCT                                                                                       <  1:91027/129‑1                                                         GATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTA                                                                                      <  2:235264/129‑1                                                                    AAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTA                                                                           <  2:118172/129‑1                                                                                                   GAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTT                                             <  1:228735/129‑1                                                                                                               ATTGTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACGTTGTAACAACAGTATTTATTGTGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCT                                 <  1:228195/129‑1                                                                                                                      GTTAAAAGTCTTCATTTTGGATACATAGAAATCTTGTAATAACAGTATTTATTGGGTTTGGAGTCCCTAGTGTGTCTCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAA                          <  2:101977/129‑1                                                                                                                                  CAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTA              <  1:176238/129‑1                                                                                                                                       TGGATATATTGAATCCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCTTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAATTTTTTCTTCTAACAAA         <  2:99724/129‑1                                                                                                                                            ACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCATCCTAAAATTTTTCTTCTAACAAATGAGA    >  1:133034/1‑129                                                                                                                                              ATAGAAACCTTGTAACAACAGTATTTCTTGGGTTTGCCGTCCCTAATGGGTCCCTAAATTACAAACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAAT  >  1:137935/1‑129                                                                                                                                                                                                                                                                                TTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTA‑TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2085436‑2085296 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAAT  <  USA300TCH1516_ALE/2128343‑2128216

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.