New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2023587 =	93 (0.950)	8 (0.090)	6/148	NT	9.1%	coding (200/207 nt)	USA300HOU_RS10200	hypothetical protein
	?	USA300TCH1516_ALE	2023639 =	73 (0.800)					coding (148/207 nt)	USA300HOU_RS10200	hypothetical protein

AGAATTAACAGATATATATGATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2023682‑2023587 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgacaATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCATTTGCATTTTTATATTTTTCAGGATCTAATAATCCTTGA  >  USA300TCH1516_ALE/2023639‑2023727                                                                                                                                                                                            AGAATTAACAGATATATATGATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑G                                                                                                >  1:2450872/1‑91  GAATTAACAGATATATATGATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GC                                                                                               >  1:1510454/1‑91   AATTAACAGATATATATGATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCG                                                                                              <  1:1584362/91‑1                     ATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTT‑‑‑‑‑CACTTGGCGACAATCTTTCTCTTGATTGAAC                                                                        >  1:973192/1‑91                     ATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTT‑‑‑‑‑CACTTGGCGACAATCTTTCTCTTGATTGAAC                                                                        >  1:973290/1‑91                                            TTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTT                                                     >  1:596861/1‑91                                              GTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAA                                                   >  1:2830794/1‑91                                               TCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAAT                                                  >  1:723528/1‑91                                                CGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGCACAAAATCATATATATCTGTTAATT                                                 >  1:3864911/1‑91                                                CGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATT                                                 >  1:2704623/1‑91                                                        GAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCA                                         >  1:1222973/1‑91                                                                                              GACAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCATTTGCATTTTTATATTTTTCAGGATCTAATAATCCTT    <  1:3141142/91‑1                                                                                                CAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCATTTGCATTTTTATATTTTTCAGGATCTAATAATCCTTGA  >  1:2967830/1‑91                                                                                                CAATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCATTTGCATTTTTATATTTTTCAGGATCTAATAATCCTTGA  >  1:389626/1‑91                                                                                                                                                                                            AGAATTAACAGATATATATGATTTTGTTCAATCAAGAGAAAGATTGTCGCCAAGTGAAGTGACAGCTATTGCTGACGCTTTAGGACAATT‑GCGACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2023682‑2023587 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgacaATCTTTCTCTTGATTGAACAAAATCATATATATCTGTTAATTCTTCTTCATTTGCATTTTTATATTTTTCAGGATCTAATAATCCTTGA  >  USA300TCH1516_ALE/2023639‑2023727

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