New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 399701	113 (0.910)	6 (0.050)	6/236	NT	5.4%	intergenic (+9/+83)	efeU/tatC2	Ferrous iron permease EfeU/Sec‑independent protein translocase protein TatCy
	?	USA300TCH1516_ALE	= 399706	108 (0.950)					intergenic (+14/+78)	efeU/tatC2	Ferrous iron permease EfeU/Sec‑independent protein translocase protein TatCy

ATTAGGTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/399551‑399701 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaaacaggcACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACATGTC  <  USA300TCH1516_ALE/399706‑399568                                                                                                                                                                                                                                                                                                     ATTAGGTGGGATGCCAAGAGATGTTATTGAAGGATGCCCAACGATTAACTGGTTGGGCGTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATA                                                                                                                                                        <  2:655253/141‑1  TTAGGTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAc                                                                                                                                                       <  1:1029796/141‑2  TTAGGTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAA                                                                                                                                                       >  2:1015007/1‑141    AGGTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAA                                                                                                                                                     >  1:40740/1‑141      GTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAA                                                                                                                                                   >  1:187482/1‑141      GTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAA                                                                                                                                                   >  1:509428/1‑141      GTGCGATGCCAAGACATGTTATTGAAGGATACCCAACGAATAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAA                                                                                                                                                   >  2:48342/1‑141         CGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGTCTTTTATCCAAGTTATGAACCATTAATAGCACAAGGTGCTTATATTATGGTAGTTGCTGTCTTAATCTTTAAATTTAAAAAATAAAAAACAG                                                                                                                                                <  4:387330/141‑1         CGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAG                                                                                                                                                >  3:272331/1‑141          aATGCAAAGACATGTTATTGAAGGATTCCCAACGATTAACGGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATAAAAAAAAAAAAAAACAGG                                                                                                                                               <  2:734788/140‑1           ATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGC                                                                                                                                              >  1:667545/1‑141                AAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGCACTCG                                                                                                                                         <  3:26192/141‑1                AAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTCTATCAAAGTTATGAACCATTGATAGCACAAAGTGCTTATATTATGGTAGTTCCGATCTTAAACATTAAATATAAAAAATAAAAAACAGGCACTCG                                                                                                                                         <  4:14923/141‑1                 AGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGCACTCG‑G                                                                                                                                       <  2:778854/141‑1                             GAAGGATTCCCAACGATTAACTGGTTGGGCTTTTTTCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATCATGATAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGCACCCG‑GCCTGTTTTTTAT                                                                                                                           <  4:74870/141‑1                                                                                        ACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAG                                                                                                                                                <  3:270871/62‑1                                                                                        ACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAG                                                                                                                                                >  4:270871/1‑62                                                                                                CTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGCCGAGT‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCAT                                                        >  1:775399/1‑141                                                                                                  TATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGCCGAGT‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAA                                                      >  2:480001/1‑141                                                                                                                                AAATTTAAAAAATAAAAAACAGGC‑CGAGTGCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTT                        >  3:21565/1‑141                                                                                                                                      AAAAAATAAAAAACAGGCCGAGT‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATGGCAACTATCATAATATAAGCACATTGTGCTAACAATGGTTCATAACTTGGAAAAAAGCAGAACCAGTTAATCGTTGGGAAT                  >  2:525392/1‑141                                                                                                                                                AAACACGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAA        <  4:232840/141‑1                                                                                                                                                 AACAGGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTCCCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTAGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAAC       >  2:280374/1‑141                                                                                                                                                  ACAGGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGCTAAACGCCCAACCAGTTAATCGTTCGGAATCCATCAATAACA      >  2:254571/1‑141                                                                                                                                                  ACAGGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACA      >  1:357884/1‑141                                                                                                                                                  ACAGGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACA      >  1:136897/1‑141                                                                                                                                                     GGCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACATGT   >  2:699608/1‑141                                                                                                                                                      GCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACATGTC  >  3:331738/1‑141                                                                                                                                                      GCACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACATGTC  >  1:651563/1‑141                                                                                                                                                                                                                                                                                                     ATTAGGTGCGATGCCAAGACATGTTATTGAAGGATTCCCAACGATTAACTGGTTGGGCTTTTATCCAAGTTATGAACCATTGATAGCACAAGGTGCTTATATTATGGTAGTTGCTATCTTAATCTTTAAATTTAAAAAATAAAAAACAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/399551‑399701 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaaacaggcACTCG‑GCCTGTTTTTTATTTTTTAAATTTAAAGATTAAGATAGCAACTACCATAATATAAGCACCTTGTGCTATCAATGGTTCATAACTTGGATAAAAGCCCAACCAGTTAATCGTTGGGAATCCTTCAATAACATGTC  <  USA300TCH1516_ALE/399706‑399568

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