New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 715316	107 (1.040)	4 (0.040)	4/268	7.9	3.9%	intergenic (+74/+43)	tarD/dacA	Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA
	?	USA300TCH1516_ALE	= 715335	103 (1.110)					intergenic (+93/+24)	tarD/dacA	Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGAAGTCATTTATTTAAAACGTACAGAAGGCATTTCGACGACTAAAATCAAACAAGAATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/715161‑715316 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaacggacaagttGCACATTATAAAG‑CTGCGAAACTTGTCCGTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATAGTTCTATATAATTTATTTAGCATCTTTACCATATAATTCTTGTTTGATTTTAGTCGTCGAAATGCC  <  USA300TCH1516_ALE/715335‑715189                                                                                                                                                                                                                                                                                                                  taAAGTCATTTATTTAAAACGTACAGAAGGCTTTTCGTCGACTAAAATCAAACAAGAATTATATGGTAAAGATGATGAATAAATTGTATAGAACTATCGATACTAAACGATAAATTAAATTCGATTATTATAAAATAAATATAAAttgg                                                                                                                                                             >  2:475555/3‑145       CATTTATTTAAAACGTACAGAAGGCTTTTAGACGACTAAAATCAAACAAGAATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGa                                                                                                                                                       >  1:821011/1‑148                                     GACGACTAAAATCAAACAAGAATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGTTGCACATTATAAAG‑CTGCGAAACTTGTCCG                                                                                                                        <  1:952483/149‑1                                            AAAATCAAACAAGAATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGTTGCACATTATAAAG‑CTGCAAAAATAGTCCGTTTTATA                                                                                                                 >  2:326352/1‑149                                                          ATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGTTGCACATTATAAAG‑CTGCGAAAATTGTCCGTTTTATATTTATTTTATAATA                                                                                                   >  2:866025/1‑149                                                                                                                                            TATAAATCGGACAAATTGCACAATATAAAG‑CTGCGAAACTTGTTCGTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATAGTTCTATATAAGTTATTTAGCATCTTTACCATATAATTCTTGTTTGATTTT                 <  1:326352/149‑1                                                                                                                                                AAACGGGCAAGTTGCACATTATAAAG‑CTGCGAAACTTGTCCGTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATAGTTCTATATAATTTATTTAGCATTTTTACCGTTTAATTCTGTTTTGATTTTAGTC             >  2:395193/1‑149                                                                                                                                                 AACGGACAAGTTGCACATTATAAAG‑CTGCGAAACTTGTCCGTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATAGTTCTATATAATTTATTTAGCATCTTTACCATATAATTCTTGTTTGATTTTAGTCG            <  1:691617/149‑1                                                                                                                                                          tTTGCACATTATAAAGTCTAC‑AAACTTGTCCTTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATATTTCTATATAATTTATTTAGCATCTTTACCATATAATTCTTGTTTGATTTTAGTCTTCGAAATGC   <  2:214062/148‑1                                                                                                                                                           TTGCACATTATAAAG‑CTGCGAAACTTGTCCGTTTTATATTTATTTTATAATAACCTAAGTAAATTTATCGTTTAGTATCGATAGTTCTATATCATTTATTTAGCATCTTTACCATAGAATTCTGGTTTGATTTTAGTCGTCGAAATGCC  >  2:768259/1‑149                                                                                                                                                                                                                                                                                                                  TGAAGTCATTTATTTAAAACGTACAGAAGGCATTTCGACGACTAAAATCAAACAAGAATTATATGGTAAAGATGCTAAATAAATTATATAGAACTATCGATACTAAACGATAAATTAACTTAGGTTATTATAAAATAAATATAAAACGGACAAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/715161‑715316 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaacggacaagttGCACATTATAAAG‑CTGCGAAACTTGTCCGTTTTATATTTATTTTATAATAACCTAAGTTAATTTATCGTTTAGTATCGATAGTTCTATATAATTTATTTAGCATCTTTACCATATAATTCTTGTTTGATTTTAGTCGTCGAAATGCC  <  USA300TCH1516_ALE/715335‑715189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.