New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1619594 =	96 (0.770)	6 (0.050)	5/244	NT	5.9%	coding (813/816 nt)	proC	Pyrroline‑5‑carboxylate reductase
	?	USA300TCH1516_ALE	1619661 =	102 (0.870)					intergenic (+64/+41)	proC/rnz	Pyrroline‑5‑carboxylate reductase/Ribonuclease Z

TTTAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1619740‑1619594 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttttatAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTGTATT  >  USA300TCH1516_ALE/1619661‑1619800                                                                                                                                                                                                                                                                                                 TTTAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAGAGTAATAAACAATGCTTGCCAAATAAGAATATATTATAAAAATAACCCGTCAAACACAGTGTTTGCGATGATGCATACTTGTGTTGGCGGGTTTGT                                                                                                                                                    <  4:224749/141‑1   TAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTT                                                                                                                                                  <  4:374891/141‑1   TAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTT                                                                                                                                                  >  4:144492/1‑141   TAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTT                                                                                                                                                  >  3:276866/1‑141   TAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTT                                                                                                                                                  <  2:1069765/141‑1     atgTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                <  1:223609/138‑1     ATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATATCCCGTCAAACACAGTGCTTGCGATTATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                <  1:223837/141‑1     ATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                <  1:787943/141‑1     ATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                <  3:6825/141‑1     ATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                >  2:352415/1‑141     ATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTT                                                                                                                                                >  2:539209/1‑141      TTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTA                                                                                                                                               <  3:367894/141‑1       TTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTAT                                                                                                                                              <  2:873006/141‑1                                                                          ATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTT                                                                           >  2:398487/1‑141                                                                                 ATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAA                                                                    >  3:345778/1‑141                                                                                           CCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTA                                                          >  1:344331/1‑141                                                                                           CCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGG‑TTATTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAG                                                         >  2:1020684/1‑141                                                                                                 AAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGG‑TTATTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTAT                                                   >  3:86964/1‑141                                                                                                     ACAGTGCTTGCGATGATGCATACATGTGTTTGACGGGTTATTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGCGTATCTT                                                >  4:258937/1‑141                                                                                                                                             TTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTC        <  2:223837/141‑1                                                                                                                                             TTTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTC        <  2:223609/141‑1                                                                                                                                              TTTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCT       <  1:124036/141‑1                                                                                                                                               TTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTG      <  1:720677/141‑1                                                                                                                                               TTTATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTG      <  4:206320/141‑1                                                                                                                                                  ATAATTTATTGTTATTTGGCAAGTATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTGTAT   <  1:828941/141‑1                                                                                                                                                  ATAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTGTAT   >  2:623808/1‑141                                                                                                                                                   TAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTCTCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTCTGTATCAATGTTTGATAAATTTCATTTCGATCCTCTGTCTT  >  2:390488/1‑141                                                                                                                                                                                                                                                                                                 TTTAATTTTGTAAAAGATTTTGATAGTTTTAAAATCTAATGACAAAGTAATAAACAATGCTTGCCAAATAACAATAAATTATAAAAATAACCCGTCAAACACAGTGCTTGCGATGATGCATACATGTGTTGGCGGGTTTGTTTTTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1619740‑1619594 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttttatAATTTATTGTTATTTGGCAAGCATTGTTTATTACTTTGTCATTAGATTTTAAAACTATCAAAATCTTTTACAAAATTAAAATTAGGTGTATCTTCATTTTGTATCAATGTTTGATAAATTTCATTTATATCTTCTGTATT  >  USA300TCH1516_ALE/1619661‑1619800

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