New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1789630 =	44 (0.950)	6 (0.140)	6/238	NT	13.9%	intergenic (‑111/+59)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase
	?	USA300TCH1516_ALE	1789673 =	34 (0.800)					intergenic (‑154/+16)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase

ATACCATTAATTGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAAT  >  USA300TCH1516_ALE/1789491‑1789764                                                                                                                                            |                                                                                                                                       agccgaatggccgatcatgttatcgataatttaggggataaacttgaattaaaacaaaaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAg                                                                                                                                       <  1:243678‑M1/2‑1 (MQ=255)           ttGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCAttactta                                                                                                                             >  2:233669/1‑141 (MQ=255)                   ttCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATc                                                                                                                     <  2:305569/141‑1 (MQ=255)                      gTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAAc                                                                                                                  <  1:394190/141‑1 (MQ=255)                        tGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAAcgc                                                                                                                <  1:659508/141‑1 (MQ=255)                         gataatttaggggataaacttgaattaaaacaaaaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAAcgcg                                                                                                               >  1:127066‑M1/116‑141 (MQ=255)                               ttaggggataaacttgaattaaaacaaaaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGcgtacgta                                                                                                         >  2:14303‑M1/110‑141 (MQ=255)                               aaaaGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGcgtacgta                                                                                                         <  1:353624/141‑1 (MQ=255)                                 aggggataaacttgaattaaaacaaaaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTaaa                                                                                                       >  1:185354‑M1/108‑141 (MQ=255)                                     aCCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTaa                                                                                                   >  1:487941/1‑141 (MQ=255)                                     aCCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTaa                                                                                                   >  1:612163/1‑141 (MQ=255)                                      aaacacttgaattaaaacaaaaccttgagggattgatagaagaagaaggttatattgaaaagccgaattactgagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTAAAGTAAt                                                                                                  >  2:183161‑M1/103‑141 (MQ=255)                                       taaacttgaattaaaacaaaaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATg                                                                                                 >  1:149342‑M1/102‑141 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:285543/141‑1 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:285579/141‑1 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:326716/141‑1 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:696198/141‑1 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:550761/141‑1 (MQ=255)                                         cTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGAc                                                                                               <  1:543895/141‑1 (MQ=255)                                          ttGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACt                                                                                              <  1:165808/141‑1 (MQ=255)                                                         tataCTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAat                                                                               <  2:182791/141‑1 (MQ=255)                                                            aCTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATAtt                                                                            >  2:329643/1‑141 (MQ=255)                                                              tttATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTAGGTAAAGTAATGACTTATTTATAGTGTAATATTaa                                                                          >  1:727823/1‑141 (MQ=255)                                                               ttATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAt                                                                         >  1:356221/1‑141 (MQ=255)                                                                tATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtc                                                                        <  1:524687/141‑1 (MQ=255)                                                                tATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtc                                                                        <  1:524693/141‑1 (MQ=255)                                                                tATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtc                                                                        <  2:213979/141‑1 (MQ=255)                                                                    gAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtcttct                                                                    <  2:207938/141‑1 (MQ=255)                                                                       ttAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtcttcttct                                                                 >  1:35857/1‑141 (MQ=255)                                                                        gttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTtctc                                                                >  1:70211‑M1/69‑141 (MQ=255)                                                                               gCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAAtt                                                         <  1:625576/141‑1 (MQ=255)                                                                                  tattatATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCgg                                                      <  1:649044/141‑1 (MQ=255)                                                                                      atatGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCttt                                                  >  2:192599/1‑141 (MQ=255)                                                                                        atGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTc                                                >  1:172839/1‑141 (MQ=255)                                                                                         tGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCa                                               >  2:186826/1‑141 (MQ=255)                                                                                                   aaGCGTTTTCCGTTGATTTATTTCTTTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACctt                                     <  1:367351/141‑1 (MQ=255)                                                                                                   aaGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACctt                                     >  1:390722/1‑141 (MQ=255)                                                                                                   aaGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACctt                                     >  1:483886/1‑141 (MQ=255)                                                                                                   aaGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACctt                                     <  2:175612/141‑1 (MQ=255)                                                                                                     gCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTGTTCAATATAACcttct                                   <  1:119638/141‑1 (MQ=255)                                                                                                                   tttatttaTCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAAtct                     <  1:674648/141‑1 (MQ=255)                                                                                                                          atCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAgg              <  1:584945/141‑1 (MQ=255)                                                                                                                            cTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt            <  1:277016/141‑1 (MQ=255)                                                                                                                            cTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt            <  1:517783/141‑1 (MQ=255)                                                                                                                                tttATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgt        <  1:224013/141‑1 (MQ=255)                                                                                                                                 ttATAAAAAATAGTCATTACTTACATACATCAACGCGTACTTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgtt       <  1:149306/141‑1 (MQ=255)                                                                                                                                  tataAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgttt      <  1:96710/141‑1 (MQ=255)                                                                                                                                   ataAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAATAATGCCTTATTTATAGAGTAACTTTACTCTTCTTCTCCGCAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgtttt     <  1:590505/141‑1 (MQ=255)                                                                                                                                      aaaaaTAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTCTTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACCCTCTCTCAAGGTTTTGTATTAAt  >  1:511437/1‑141 (MQ=255)                                                                                                                                      aaaaaTAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAAt  >  1:25738/1‑141 (MQ=255)                                                                                                                                      aaaaaTAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAAt  >  1:739776/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                       ATACCATTAATTGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAAT  >  USA300TCH1516_ALE/1789491‑1789764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.