New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1856676	26 (0.750)	5 (0.150)	5/254	4.1	16.7%	intergenic (‑361/+339)	aroA/USA300HOU_1728	bifunctional chorismate mutase/3‑deoxy‑7‑phosphoheptulonate synthase/hypothetical protein
	?	CP000730	1856683 =	25 (0.760)					intergenic (‑368/+332)	aroA/USA300HOU_1728	bifunctional chorismate mutase/3‑deoxy‑7‑phosphoheptulonate synthase/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTTAAAATGT  >  CP000730/1856544‑1856818                                                                                                                                            |                                                                                                                                         aaGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGtat                                                                                                                                         >  2:181038/1‑141 (MQ=255)         ttattaTAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAatat                                                                                                                                 <  2:280672/141‑1 (MQ=255)               taGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCt                                                                                                                           <  2:439764/141‑1 (MQ=255)               taGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCt                                                                                                                           <  2:368168/141‑1 (MQ=255)                 gCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCtat                                                                                                                         <  1:398787/141‑1 (MQ=255)                      ttttGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGa                                                                                                                    >  2:74396/1‑141 (MQ=255)                        ttGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAAc                                                                                                                  <  2:174530/141‑1 (MQ=255)                         tGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACa                                                                                                                 <  2:186386/141‑1 (MQ=255)                            gTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACAtca                                                                                                              <  2:227268/141‑1 (MQ=255)                                              aaGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGc                                                                                           <  1:299598/141‑1 (MQ=255)                                                     aTTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATAttt                                                                                    >  1:355955/1‑141 (MQ=255)                                                        ttCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTaaa                                                                                 >  2:163775/1‑141 (MQ=255)                                                          cGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAAC‑‑‑‑‑‑CTTTGTATATTAATATAAATCTATAGTGAACa                                                                                                                 <  1:9342/102‑1 (MQ=255)                                                          cGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAAC‑‑‑‑‑‑CTTTGTATATTAATATAAATCTATAGTGAACa                                                                                                                 >  2:9342/1‑102 (MQ=255)                                                            tttCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAg                                                                             <  1:140948/141‑1 (MQ=255)                                                              tCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTg                                                                           <  2:191898/141‑1 (MQ=255)                                                                                   aaaaTTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTaaa                                                      >  1:412681/1‑141 (MQ=255)                                                                                    aaaTTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAAC‑‑‑‑‑‑CTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAT‑GAGCGGCTATATTTGAATTAGTGAACGTCATTGTACCTTCTAAGATTCAtt                                               >  2:195905/1‑141 (MQ=255)                                                                                      aTTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATCATAAAAACCAAAGAGC‑ACACGACTGAACTCTAGTTAAATTAGTGAACGTCATTGTACCTTCTCAAAtt                                                   >  1:172430/1‑141 (MQ=255)                                                                                           cATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTg                                              <  1:181038/141‑1 (MQ=255)                                                                                           cATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTg                                              <  2:47220/141‑1 (MQ=255)                                                                                                      ccTAACGCTTAATAAAAATTAACAAC‑‑‑‑‑‑CTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAT‑GAGCGGCTATATTTGAATTAGTGAACGTCATTGTACCTTCTAAGATTCATTGTTTATTTGATTATCGaa                             <  2:361121/141‑1 (MQ=255)                                                                                                         aaCGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATc                                >  2:436470/1‑141 (MQ=255)                                                                                                                aataaAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATAtt                         >  1:261392/1‑141 (MQ=255)                                                                                                                  taaAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATAtttt                       >  1:264410/1‑141 (MQ=255)                                                                                                                  taaAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATAtttt                       <  2:364656/141‑1 (MQ=255)                                                                                                                           acaacCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTc              >  2:403196/1‑141 (MQ=255)                                                                                                                                ctttgtctttgtATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCtt         >  2:53827/1‑141 (MQ=255)                                                                                                                                ctttgtctttgtATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCtt         >  2:96037/1‑141 (MQ=255)                                                                                                                                      ctttgtATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTTAAAAtg   <  1:175298/141‑1 (MQ=255)                                                                                                                                       tttgtATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTTAAAAtgt  <  2:355955/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                         AAGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTTAAAATGT  >  CP000730/1856544‑1856818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.