New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2492466 =	95 (1.000)	5 (0.060)	5/244	10.6	5.8%	intergenic (+9/+37)	yhfP/rimI_4	Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase
	?	USA300TCH1516_ALE	2492499 =	76 (0.880)					intergenic (+42/+4)	yhfP/rimI_4	Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTGAGAGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2492615‑2492466 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gatgtctttttTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTATGTACTCTCAACAGCCACACCTTTAATA  >  USA300TCH1516_ALE/2492499‑2492632                                                                                                                                                                                                                                                                                              TTGAGAGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGA                                                                                                                                                 <  1:80736/141‑1  TGAGAGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGAT                                                                                                                                                <  2:560574/141‑1   GAGAGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATG                                                                                                                                               >  4:305878/1‑141      AGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCT                                                                                                                                            >  2:646151/1‑141      AGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCT                                                                                                                                            <  3:125493/141‑1       GTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTT                                                                                                                                           >  2:683433/1‑141         ACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTTTT                                                                                                                                         >  2:397248/1‑141                                                                                                              CTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCT                                                                                                     >  3:7832/1‑76                                                                                                              CTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCT                                                                                                     <  4:7832/76‑1                                                                                                                   TTAAAAAAGACATCTCGCATAACGGGATGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCG                                                          >  1:425786/1‑114                                                                                                                   TTAAAAAAGACATCTCGCATAACGGGATGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCG                                                          <  2:425786/114‑1                                                                                                                     AAAAAAGACATCTCGCATAACGGGATGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTAT                             >  1:395156/1‑141                                                                                                                                              TGTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTATGTACTCTCAACAGCCACACCTTTAA    <  2:267978/141‑1                                                                                                                                               GTCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTATGTACTCTCAACAGCCACACCTTTAAT   <  2:416497/141‑1                                                                                                                                                TCTTTTTTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTATGTACTCTCAACAGCCACACCTTTAATA  <  2:689161/141‑1                                                                                                                                                                                                                                                                                              TTGAGAGTACATACGTTAGTCTGATTGCAGACTACCCAGCGGATAAATTATATACAAAATTTGGATTTATACCTACCGAACCAGATTCAGGCGGTATGTATATCAAATACTAAATTAAAAAAGACATCTCGCATAACGGGATGTCTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2492615‑2492466 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gatgtctttttTAATTTAGTATTTGATATACATACCGCCTGAATCTGGTTCGGTAGGTATAAATCCAAATTTTGTATATAATTTATCCGCTGGGTAGTCTGCAATCAGACTAACGTATGTACTCTCAACAGCCACACCTTTAATA  >  USA300TCH1516_ALE/2492499‑2492632

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.