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

TATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGATCGGCCATTCGGCT  >  USA300TCH1516_ALE/1789547‑1789811                                                                                                                               |                                                                                                                                           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                                                                                                                       <  1:524693/141‑1 (MQ=255)        tATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAAtc                                                                                                                       <  1:524687/141‑1 (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)                                                      gagaagaagattaatattacactataaataagtcattactttacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAAc                                                                         >  1:70211‑M2/74‑141 (MQ=255)                                                           tttatttaTCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAAtct                                                                    <  1:674648/141‑1 (MQ=255)                                                                  atCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAgg                                                             <  1:584945/141‑1 (MQ=255)                                                                    cTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt                                                           <  1:517783/141‑1 (MQ=255)                                                                    cTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt                                                           <  1:277016/141‑1 (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)                                                                                       cattactttacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTa                                        >  1:149342‑M2/41‑141 (MQ=255)                                                                                       CATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTa                                        <  2:57379‑M1/141‑1 (MQ=255)                                                                                        attactttacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCAGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTATCAATCCCTCAAGGTTTTGTTTTAATTcaagtgttt                                       >  2:183161‑M2/40‑137 (MQ=255)                                                                                             tttacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCt                                  >  1:185354‑M2/35‑141 (MQ=255)                                                                                               tacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTaa                                >  2:14303‑M2/33‑141 (MQ=255)                                                                                                catacatCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTaaa                               <  2:118283/141‑1 (MQ=255)                                                                                                  tacatCAACGCGTACGTAAAGTAATGACTTATTTATGGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAAACTTCTTATTCTAAAAATCTCTCACGGTTTTGTTTTAATTCAAGTTTATCCCCTAAAtt                             >  1:72836/1‑141 (MQ=255)                                                                                                     cgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATc                          >  1:127066‑M2/27‑141 (MQ=255)                                                                                                     atCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGCTTATCCCCTAAATTATc                          >  1:528226/1‑141 (MQ=255)                                                                                                            cgtacgtaAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACa                   >  1:19535/1‑141 (MQ=255)                                                                                                                cgtaAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGAt               >  1:8352/1‑141 (MQ=255)                                                                                                                             ctTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGATCGGCCATTCGGCt  <  1:243678‑M2/139‑1 (MQ=255)                                                                                                                               |                                                                                                                                           TATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGATCGGCCATTCGGCT  >  USA300TCH1516_ALE/1789547‑1789811

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.