New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1735361	41 (0.890)	4 (0.100)	4/234	NT	9.8%	intergenic (+61/+100)	USA300TCH1516_01624/tcdA	putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase
	?	USA300TCH1516_ALE	= 1735390	37 (0.890)					intergenic (+90/+71)	USA300TCH1516_01624/tcdA	putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase

AAAACAAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1735209‑1735361 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaactgactagtTCGCAAGCATAGTAGAATATGCCTCGTGTACTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTGTTTAAGTAAGTTGTTATATATTTCTTTGAGTTGTTGTT  <  USA300TCH1516_ALE/1735390‑1735251                                                                                                                                                                                                                                                                                                       AAAACAAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCA                                                                                                                                                          >  1:769170/1‑141  AAACAAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAA                                                                                                                                                         >  2:70735/1‑141  AAACAAAATTTATTACGAACCAAAAACGACATCGAAAAGTGAACAACAACACAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAA                                                                                                                                                         <  1:111764/141‑1    ACAAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAA                                                                                                                                                       <  2:126802/141‑1      AAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACT                                                                                                                                                     >  1:25890/1‑141       AAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTG                                                                                                                                                    <  2:47443/141‑1       AAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTG                                                                                                                                                    <  2:47420/141‑1         ATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGAC                                                                                                                                                  >  1:91336/1‑141          TTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACT                                                                                                                                                 <  2:175959/141‑1             ATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGT                                                                                                                                              >  1:740065/1‑141                                         TGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTTCGCAAGCATAGTAGAATATGCCTCGTG                                                                                                                  <  2:308251/141‑1                                          GAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTTCGCAAGCATAGTAGAATATGCCTCGTGT                                                                                                                 <  1:182276/141‑1                                            ACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTTCGCAAGCATAGTAGAATATGCCTCGTGTAC                                                                                                               <  1:456317/141‑1                                                                                                                   tcTGATATTTTTGCTATAATCAAATCAAAACTGACTCGTTCGCAAGAATAGTAGAATATGCCTCGTGTACTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTG                                        <  1:398453/139‑1                                                                                                                                                 CTGACTAGTTCGCAAGCATAGTAGAATATGCCTCGTGTACTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTGTTTAAGTAAGTTGTTATATATTTCTTTGAG          <  1:444644/141‑1                                                                                                                                                      TAGTTCGCAAGCATAGTAGAATATGCCTCGTGTATTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTGTTTAAGTAAGTTGTTATATATTTCTTTGAGTTGTT     <  1:729402/141‑1                                                                                                                                                         TTCGCAAGCATAGTAGAATATGCCTCGTGTACTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTGTTTAAGTAAGTTGTTATATATTTCTTTGAGTTGTTGTT  <  1:759315/141‑1                                                                                                                                                                                                                                                                                                       AAAACAAAATTTATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1735209‑1735361 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaactgactagtTCGCAAGCATAGTAGAATATGCCTCGTGTACTAGTCAGTTTTGATTTGATTATAGCTAAAATATCAAAGGTAATCGATTTAATCTTATTTTTACGGCCTTTGTTTAAGTAAGTTGTTATATATTTCTTTGAGTTGTTGTT  <  USA300TCH1516_ALE/1735390‑1735251

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