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.

ATAAGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTT  >  CP000730/1856542‑1856811                                                                                                                                       |                                                                                                                                         aTAAGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACctttgtctttgt                                                                                                                                    >  1:91323/1‑141 (MQ=255)   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)                                                                                                                                       |                                                                                                                                         ATAAGTGTCATTATTATAGCTTATTTTGAGTCAACATTACTGCTTTTAAGAAAAATTTTCGTTTCTATCTTCTATTATAAATCTAAAATTCTCATACATTCAACCTAACGCTTAATAAAAATTAACAACCTTTGTCTTTGTATATTAATATAAATCTATAGTGAACATCACTCACCAACAC‑ATTCAGCTATATTTAAATTAGTGAACGTCATTGTACCTTCTAAAATTCATTGTTTATTTGATTATCGAATATTTTTCCATCTTCAGCTT  >  CP000730/1856542‑1856811

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.