New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2001491 =	7 (0.110)	6 (0.100)	4/246	NT	47.5%	intergenic (‑3219/+116)	USA300TCH1516_01882/USA300TCH1516_01883	tRNA‑Val/tRNA‑Ala
	?	USA300TCH1516_ALE	2179606 =	NA (NA)					intergenic (+3368/+1927)	ilvA/USA300TCH1516_02069	L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly

CTAGTGCCAAGGCATCCACCGTGCGCCCTTAATAACTTAATCTATGTTTCCACCATTTTTATAAGTCAAACGTTAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATCGAA  >  USA300TCH1516_ALE/2001352‑2001629                                                                                                                                            |                                                                                                                                           gcgagcgcttgactgaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaatcagcttgaattcataagaaataatcgctagtgttcgtaaGa                                                                                                                                           >  1:548005‑M1/140‑141 (MQ=255)  cgagcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtcaaagatatattttaccaagcaaaaccgagtgaataaagaggtttaaataagcttgaattcagaagaaataatcgctagtgttcgaaaGaa                                                                                                                                          <  1:445221‑M1/3‑1 (MQ=255)  cgagcgcttgactaaaaagaaatcgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGaa                                                                                                                                          >  1:136315‑M1/139‑141 (MQ=255)   gagcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAac                                                                                                                                         >  1:392835‑M1/138‑141 (MQ=255)    aggccttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAaca                                                                                                                                        >  1:355571‑M1/137‑141 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                       <  1:414082‑M1/6‑1 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                       >  1:637809‑M1/136‑141 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                       >  1:637942‑M1/136‑141 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagaggtttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                       <  2:251689‑M1/6‑1 (MQ=255)      cgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGaacacc                                                                                                                                      <  1:704363‑M1/7‑2 (MQ=255)      cgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAACACt                                                                                                                                      <  2:120677‑M1/7‑1 (MQ=255)         ttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaagaacacccaa                                                                                                                                   <  2:402961‑M1/10‑5 (MQ=255)                      atttgtaccttgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaatacgcttcaattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTAt                                                                                                                      >  2:44382‑M1/119‑141 (MQ=255)                      atttgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTAt                                                                                                                      >  2:476377‑M1/119‑141 (MQ=255)                      aattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTAt                                                                                                                      >  2:476387‑M1/119‑141 (MQ=255)                              attgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTATGAATTCaa                                                                                                              >  2:631842‑M1/111‑141 (MQ=255)                                 tatcTTATTCTATGTTTTCACCATTTTTATAAGTCAGACGTTAACATGATTTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCt                                                                                                           <  1:535795/138‑1 (MQ=1)                                              ataattaaaatatagatcacaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAActct                                                                                              >  2:763854‑M1/95‑141 (MQ=255)                                                                       cggtAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTACTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCTGTTTTGCTTGGTaa                                                                     <  2:523909/138‑1 (MQ=0)                                                                                                                           atcgctagtgttcgaaaGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTTAATGTACAAATAATGGTggaa                 <  2:510868‑M1/124‑2 (MQ=255)                                                                                                                              gtgAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACt              <  1:4465/141‑1 (MQ=33)                                                                                                                              gtgAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACt              <  2:58197/141‑1 (MQ=33)                                                                                                                                 aGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGc           <  1:415702/141‑1 (MQ=35)                                                                                                                                     ttCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGa       <  2:305760/141‑1 (MQ=39)                                                                                                                                     ttCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGa       >  2:73739/1‑141 (MQ=39)                                                                                                                                       cTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATc     >  2:524244/1‑141 (MQ=40)                                                                                                                                         ttCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATCGa   >  1:743029/1‑141 (MQ=255)                                                                                                                                          tCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATCGaa  >  1:214731/1‑141 (MQ=255)                                                                                                                                          tCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTCACTTATCTCGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATCGaa  >  2:366002/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                           CTAGTGCCAAGGCATCCACCGTGCGCCCTTAATAACTTAATCTATGTTTCCACCATTTTTATAAGTCAAACGTTAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGATCGAA  >  USA300TCH1516_ALE/2001352‑2001629

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.