New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2467825 =	221 (1.160)	20 (0.110)	14/150	NT	9.3%	intergenic (+42/+66)	USA300HOU_RS12705/lipY	hypothetical protein/Triacylglycerol lipase
	?	USA300TCH1516_ALE	2467878 =	185 (1.040)					intergenic (+95/+13)	USA300HOU_RS12705/lipY	hypothetical protein/Triacylglycerol lipase

TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2467919‑2467825 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgggtCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGGAT  >  USA300TCH1516_ALE/2467878‑2467967                                                                                                                                                                                           TAGGTGAGGAGGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  2:864320/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  2:870226/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  2:2003913/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  2:1845392/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  1:3384295/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  1:3344671/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  1:3144851/1‑91 TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATT                                                                                                >  1:2720080/1‑91  AGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTG                                                                                               >  1:1237856/1‑91  AGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTG                                                                                               >  2:3370448/1‑91  AGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTG                                                                                               >  1:1237771/1‑91   GATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGG                                                                                              <  1:2858126/91‑1   GATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGG                                                                                              >  2:3196891/1‑91    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:3454584/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:1375498/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:1161097/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  1:790637/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:2181336/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:37199/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  2:1863783/91‑1    ATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGG                                                                                             <  1:694980/91‑1     TGAGGATGTAATACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  2:1825962/91‑1     TGAGGATGTAACACAAAATAACTAGTAACATATAAATGACCCAGTTACGATTTCATGCAAGTTGATATTTGACATGAAAACGTGATTGGGT                                                                                            <  2:3617599/91‑1     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            >  1:528302/1‑91     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  2:2569280/91‑1     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            >  2:2618081/1‑91     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  1:346816/91‑1     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  1:1313495/91‑1     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  1:1318377/91‑1     TGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT                                                                                            <  1:3163112/91‑1      GAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGATACGATTTCACGCAAGATGATATATGACATGAAAACGTAATTGGGca                                                                                           >  2:41300/1‑89                                   TATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTA                                                              >  2:152607/1‑91                                         TGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCT                                                        >  2:1578762/1‑91                                          GACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTC                                                       >  1:895053/1‑91                                          GACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTC                                                       >  2:1816522/1‑91                                                 TTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATC                                                >  1:863745/1‑91                                                 TTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTAATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATC                                                >  1:3865957/1‑91                                                   ACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGA                                              >  1:712636/1‑91                                                    CGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGAT                                             >  2:1547002/1‑91                                                    CGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGAT                                             >  2:3495472/1‑91                                                     GATTTCATGCAAGATGATATTTGACATGAAAACGTAACTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATT                                            >  2:2603222/1‑91                                                      ATTTCATGCAAGCTGATATTTGACATGAAAACGTAACTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTT                                           >  1:2995211/1‑91                                                      ATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTT                                           >  1:3053127/1‑91                                                      ATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTT                                           >  1:1889961/1‑91                                                       TTTCATGCAAGATGATATTTGACATGAAATCGTAACTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTG                                          >  2:1085558/1‑91                                                        TTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGG                                         <  2:1889961/91‑1                                                        TTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGG                                         <  2:3053127/91‑1                                                            TGCAAGATGATATTTGACATGAAATCGTAACTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAAT                                     >  2:1785305/1‑91                                                             GCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTA                                                  >  2:3265171/1‑77                                                             GCAAGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTA                                                  <  1:3265171/77‑1                                                                AGATGATATTTGACATGAAAACGTAATTGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGT                                 >  1:3716100/1‑91                                                                                           TGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATT      <  2:3664354/91‑1                                                                                           TGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATT      <  1:3663037/91‑1                                                                                           TGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATT      >  2:3329917/1‑91                                                                                           TGGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATT      <  2:359504/91‑1                                                                                            GGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTG     <  1:3142050/91‑1                                                                                            GGGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTG     <  1:1450248/91‑1                                                                                             GGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGG    <  2:2061456/91‑1                                                                                             GGTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGG    >  1:1728656/1‑91                                                                                              GTCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGGA   >  1:1386161/1‑91                                                                                               TCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTGATTGGAT  >  1:1936093/1‑91                                                                                               TCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGGAT  >  1:1499463/1‑91                                                                                                                                                                                           TAGATGAGGATGTAACACAAAATAACTAATAACATATAAATGACCCAGTTACGATTTCATGCAAGATGATATTTGACATGAAAACGTAATTGGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2467919‑2467825 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgggtCATTTATATGTTATTAGTTATTTTGTGTTACATCCTCATCTATCGATTTGGCAATTTGTTTAATAGCTTTATGTGATTGTCTAATTGGAT  >  USA300TCH1516_ALE/2467878‑2467967

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