New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	511377 =	48 (1.040)	3 (0.070)	3/246	NT	6.1%	coding (42/597 nt)	recR	Recombination protein RecR
	?	USA300TCH1516_ALE	511430 =	47 (1.080)					coding (95/597 nt)	recR	Recombination protein RecR

ATGTGACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCATA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/511523‑511377 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttcataCCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTCACATTACTGAAAATGATCCATGTTATATTTGTGAAGATAAGCAAAGA  >  USA300TCH1516_ALE/511430‑511566                                                                                                                                                                                                                                                                                              ATGTGACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAAT                                                                                                                                                 >  1:239732/1‑141     GACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCA                                                                                                                                             <  1:698382/141‑1     GACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCA                                                                                                                                             <  2:175196/141‑1      ACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCAT                                                                                                                                            <  2:95327/141‑1                                                                                        TCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCATACCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCGAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCG                                                          >  1:618214/1‑141                                                                                                 TGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCATACCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTC                                                 >  1:329039/1‑141                                                                                                        CCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCATACCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTCACATTAC                                          >  2:100361/1‑141                                                                                                                                          gctgTTCATACCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTCACATTACTGAAAATGATCCATGTTATATTTGTGAAGATAAG        <  1:507461/137‑1                                                                                                                                                CATACCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTCACATTACTGAAAATGATCCATGTTATATTTGTGAAGATAAGCAAAGA  >  1:52179/1‑141                                                                                                                                                                                                                                                                                              ATGTGACCACATACGCTACAATATGTTAATTCTCTCTTAACATCTACTAATGCTTTGGCAAACTGAACAACATCGTCTTCTTTCATATCTAAGGTATGAAAAGCCAGACGTTGGGCTGTCTTTGGACCAATGCCTGGCAATTTCATA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/511523‑511377 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttcataCCTTAGATATGAAAGAAGACGATGTTGTTCAGTTTGCCAAAGCATTAGTAGATGTTAAGAGAGAATTAACATATTGTAGCGTATGTGGTCACATTACTGAAAATGATCCATGTTATATTTGTGAAGATAAGCAAAGA  >  USA300TCH1516_ALE/511430‑511566

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.