New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	62771 =	31 (0.250)	9 (0.080)	5/240	NT	34.1%	intergenic (‑238/+275)	USA300TCH1516_00053/speG	hypothetical protein/Spermidine N(1)‑acetyltransferase
	?	USA300TCH1516_ALE	62827 =	6 (0.050)					intergenic (‑294/+219)	USA300TCH1516_00053/speG	hypothetical protein/Spermidine N(1)‑acetyltransferase

GATGACGCTGTAACAACGGTACTTAATAACGATTTGCAAACAATTATTAATGACTATCTATCAGAATGAAGCTTATATTAATTTCAACAAAAAT‑‑‑‑‑‑AGAGCATCCTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/62912‑62771 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tatttttgtTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGACAT  >  USA300TCH1516_ALE/62827‑62964                                                                                                                                                                                                                                                                                                GATGACGCTGTAACAACGGTACTTAATAACGATTTGCAAACAATTATTAATGACTATCTATCAGAATGAAGCTTATATTAATTTCAACAAAAAT‑‑‑‑‑‑AGAGCATCCTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTG                                                                                                                                             >  1:684011/1‑141                                               TTAATGACTATCTATCAGAATGAAGCTTATATTAATTTCAACAAAAATAAATTGAGAGCATCCTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTA                                                                                                     >  3:132107/1‑141                                                                                                           TCCTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCC                                         >  1:181751/1‑141                                                                                                             CTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTTTTTTTATTTATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                                       >  2:499008/1‑141                                                                                                             CTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                                       >  1:222210/1‑141                                                                                                             CTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                                       >  2:667013/1‑141                                                                                                             CTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                                       >  2:667084/1‑141                                                                                                             CTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                                       >  2:756476/1‑141                                                                                                              TTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACGGCGTCATCATTCATAAAATCCTCG                                      >  1:796004/1‑141                                                                                                                   TTTGCGGTAAGGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGAT                                 >  3:196131/1‑141                                                                                                                                             ATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACA       <  3:295542/141‑1                                                                                                                                             ATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACA       <  2:320167/141‑1                                                                                                                                              TTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAG      <  2:638064/141‑1                                                                                                                                               TTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTATCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGA     >  4:225506/1‑141                                                                                                                                               TTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGA     >  3:195913/1‑141                                                                                                                                                TTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTAATCTGAACCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGAC    <  1:1062794/141‑1                                                                                                                                                  TGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGACAT  <  1:338474/141‑1                                                                                                                                                                                                                                                                                                GATGACGCTGTAACAACGGTACTTAATAACGATTTGCAAACAATTATTAATGACTATCTATCAGAATGAAGCTTATATTAATTTCAACAAAAAT‑‑‑‑‑‑AGAGCATCCTTCACTTTGCGGTAAGGGATGCTCTCAATTTATTTTTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/62912‑62771 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tatttttgtTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCCTCTTACAGACAT  >  USA300TCH1516_ALE/62827‑62964

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.