New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 260294	49 (0.770)	3 (0.050)	3/238	NT	6.1%	intergenic (‑408/‑180)	potD_1/pflB	Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase
	?	USA300TCH1516_ALE	= 260312	48 (0.820)					intergenic (‑426/‑162)	potD_1/pflB	Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase

TTTAATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/260146‑260294 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttgtgtaacagTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAAGATTT  <  USA300TCH1516_ALE/260312‑260175                                                                                                                                                                                                                                                                                                     ttgAATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTCATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTG                                                                                                                                                        <  2:643948/138‑1   TAATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATAGTCCTAAGTTAACGTTGAAAGCAATGAAAATAGTGAACATTATAACTGTTGTG                                                                                                                                                      <  2:755168/141‑1    AATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGT                                                                                                                                                     <  1:558946/141‑1     ATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTA                                                                                                                                                    <  2:589/141‑1      TCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAA                                                                                                                                                   >  2:320335/1‑141       CCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAAC                                                                                                                                                  <  1:700220/141‑1         AGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG                                                                                                                                                <  1:660738/141‑1         AGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG                                                                                                                                                <  2:652654/141‑1                                         AGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAGTAATATGCTAATT‑AC‑‑ATT‑CTGTTACACAACAG                                                                                                            >  2:381563/1‑141                                                                                         TACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑‑A‑ATGCAATTA‑GCATATTACTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTA                                                             <  2:629436/140‑1                                                                                         TACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑‑A‑ATGC‑AATTAGCATATTACTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTA                                                             >  1:629436/1‑140                                                                                                                                            TGTGTAACAGTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGA         >  2:462013/1‑141                                                                                                                                            TGTGTAACAGTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGA         >  2:462321/1‑141                                                                                                                                              TGTAACAGTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAA       >  1:461531/1‑141                                                                                                                                                  ACATTAATATTCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAAGATT   <  1:275238/141‑1                                                                                                                                                  ACAGTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAAGATT   >  1:505311/1‑141                                                                                                                                                   CAGTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAAGATTT  >  1:568920/1‑141                                                                                                                                                                                                                                                                                                     TTTAATCCAGTCTCTTCATATATAAAAGTAAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/260146‑260294 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttgtgtaacagTAATATGCTAATT‑GC‑‑ATT‑CTGTTACACAACAGTTATAATGTTCACTATTTTCATTGCTTTAAAAGTTAATTTAGGAGTATATATTTGTTTATAAAAAATGATTGTTGATAAGCGTTAAATCAACACTTAGAAAGATTT  <  USA300TCH1516_ALE/260312‑260175

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.