New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1470044	NA (NA)	15 (0.160)	9/150	NT	14.4%	intergenic (‑91/‑254)	USA300TCH1516_01369/rnhA	hypothetical protein/14.7 kDa ribonuclease H‑like protein
	?	USA300TCH1516_ALE	= 2866850	95 (0.970)					intergenic (‑249/+204)	USA300HOU_RS14695/noc_2	hypothetical protein/Nucleoid occlusion protein

CGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGAAG  >  USA300TCH1516_ALE/1469987‑1470133                                                          |                                                                                          cGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCACATTTTCGTTCAGTCAACTACTGCCAATATAACAt                                                          <  1:1052822/91‑1 (MQ=17)    aaTTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGt                                                       <  1:963052/91‑1 (MQ=34)    aaTTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGt                                                       <  1:2369296/91‑1 (MQ=34)        ctctGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTagag                                                   >  1:334589/1‑91 (MQ=33)          ctGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCa                                                 >  1:3938179/1‑91 (MQ=34)          ctGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCa                                                 >  1:2389681/1‑91 (MQ=34)          ctGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCa                                                 >  1:2389680/1‑91 (MQ=34)           tgtgTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCAt                                                >  1:861158/1‑91 (MQ=34)            gtgtTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATa                                               >  1:3608267/1‑91 (MQ=34)            gtgtTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATa                                               <  1:4078025/91‑1 (MQ=33)            gtgtTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATa                                               >  1:1786968/1‑91 (MQ=34)               ttGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGaa                                            <  1:973227/91‑1 (MQ=34)                tGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAAc                                           <  1:1933213/91‑1 (MQ=34)                 ggggCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACa                                          <  1:3028884/91‑1 (MQ=34)                   ggCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACAtt                                        >  1:3905389/1‑91 (MQ=34)                   ggCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACAtt                                        >  1:2663535/1‑91 (MQ=33)                    gCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTg                                       >  1:2266114/1‑91 (MQ=33)                    gCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTg                                       <  1:1368885/91‑1 (MQ=33)                      cccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAt                                     <  1:4778/91‑1 (MQ=34)                      cccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAt                                     <  1:4537/91‑1 (MQ=33)                      cccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAt                                     >  1:1419344/1‑91 (MQ=34)                      cccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAt                                     <  1:4882/91‑1 (MQ=34)                      cccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAt                                     <  1:559000/91‑1 (MQ=34)                       ccTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGAtt                                    >  1:377167/1‑91 (MQ=34)                         tGACTAGAAGTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTa                                  <  1:368875/91‑1 (MQ=18)                          gACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGTCAATATAACATCGTAGAGCATAGAACATTGATTTAt                                 >  1:3870386/1‑91 (MQ=21)                            cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGt                               <  1:2276838/91‑1 (MQ=33)                            cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGt                               <  1:717332/91‑1 (MQ=34)                            cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGt                               <  1:2718414/91‑1 (MQ=33)                            cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGt                               <  1:2578654/91‑1 (MQ=34)                            cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGt                               <  1:1764870/91‑1 (MQ=34)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCGAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:4090355/91‑1 (MQ=21)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3130670/91‑1 (MQ=34)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3130944/91‑1 (MQ=34)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             >  1:4028487/1‑91 (MQ=34)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3130713/91‑1 (MQ=34)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3130600/91‑1 (MQ=33)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3130372/91‑1 (MQ=33)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:3070027/91‑1 (MQ=33)                              aGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTcc                             <  1:1343798/91‑1 (MQ=34)                               gAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCTATATAACATCGTAGAGCATAGAACATTGATTTATGTccc                            >  1:2665210/1‑91 (MQ=21)                               gAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTccc                            >  1:199852/1‑91 (MQ=34)                                   tGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGcc                        <  1:3639630/91‑1 (MQ=33)                                   tGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGcc                        <  1:3894507/91‑1 (MQ=33)                                    gAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCt                       >  1:3764363/1‑91 (MQ=34)                                      aaaaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGa                     >  1:1241808/1‑91 (MQ=34)                                      aaaaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGa                     >  1:1337037/1‑91 (MQ=34)                                      aaaaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGa                     >  1:1337822/1‑91 (MQ=34)                                       aaaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGaa                    <  1:3144027/91‑1 (MQ=35)                                        aaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAg                   >  1:2286085/1‑91 (MQ=37)                                        aaaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAg                   >  1:581969/1‑91 (MQ=37)                                         aaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAga                  <  1:1272792/91‑1 (MQ=38)                                          aGCTTGTTACAAGCGCATTTTCGTTCAGTCAAGTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATCTCCCAGCCTGAAgat                 <  1:3537530/91‑1 (MQ=255)                                          aGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAgat                 <  1:477915/91‑1 (MQ=39)                                           gCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAgatg                >  1:249783/1‑91 (MQ=40)                                             ttGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAgatgat              >  1:3451707/1‑91 (MQ=255)                                             ttGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAgatgat              <  1:2874914/91‑1 (MQ=255)                                              tGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAtt             >  1:4124867/1‑91 (MQ=255)                                               gTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttt            <  1:1028994/91‑1 (MQ=255)                                               gTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttt            >  1:708212/1‑91 (MQ=255)                                               gTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttt            >  1:708362/1‑91 (MQ=255)                                               gTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttt            <  1:3612015/91‑1 (MQ=255)                                               gTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttt            <  1:1028993/91‑1 (MQ=255)                                                ttACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAtttt           >  1:3326454/1‑91 (MQ=255)                                                 tACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttttt          <  1:2354686/91‑1 (MQ=255)                                                 tACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttttt          <  1:2503513/91‑1 (MQ=255)                                                 tACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttttt          <  1:510084/91‑1 (MQ=255)                                                 tACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGAttttt          <  1:2504118/91‑1 (MQ=255)                                                      gcgcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAgg     >  1:1510272/1‑91 (MQ=255)                                                       cgcATTTTCGTTCAGTCAACTCCTGCCAATATAACATCGTAGAGCATAGAACATTGATTTGTGTCCCAGCCTGAAGATGATTTTTTTAGGa    <  1:2527447/91‑1 (MQ=255)                                                       cgcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGa    <  1:3946694/91‑1 (MQ=255)                                                       cgcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGa    <  1:3001584/91‑1 (MQ=255)                                                       cgcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGa    <  1:940802/91‑1 (MQ=255)                                                       cgcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGa    <  1:3001682/91‑1 (MQ=255)                                                        gcATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGaa   >  1:314532/1‑91 (MQ=255)                                                         cATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGAAg  <  1:2010435/91‑1 (MQ=255)                                                          |                                                                                          CGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACATCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGAAGATGATTTTTTTAGGAAG  >  USA300TCH1516_ALE/1469987‑1470133

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