New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1427028	41 (0.520)	4 (0.050)	4/268	8.6	9.3%	intergenic (‑759/+213)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	1442915 =	NA (NA)					intergenic (+148/+120)	USA300HOU_RS07165/USA300TCH1516_01342	TelA‑like protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGAATGTT  >  USA300TCH1516_ALE/1426926‑1427166                                                                                                       |                                                                                                                                           ggTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCAt                                                                                                      >  1:483095/1‑141 (MQ=32)                  aGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGaaa                                                                                     <  2:597127/141‑1 (MQ=32)                   gTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAAt                                                                                    <  2:520698/141‑1 (MQ=32)                             taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                          <  2:77811/141‑1 (MQ=32)                             taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                          <  2:77557/141‑1 (MQ=32)                             taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                          <  1:376821/141‑1 (MQ=32)                             taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAAGGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                          <  1:177145/141‑1 (MQ=17)                                  aaaGTTAAACGAGAGCGAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACAtt                                                                     >  1:457395/1‑141 (MQ=17)                                  aaaGTAAAACGAGAGCTAGGTTTTGTATTAATGGCAATTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACAtt                                                                     <  2:498646/141‑1 (MQ=17)                                   aaGTTAAGCGAGAGCTAGGTTTTGTATTAATGGCACTTAATATATGGAAATTAGCAGCTCAACGAGCTGTACATTATAAAAGACATATCAAAAAAGCTGATTTCCATCAAATAATTAATTGAAATCTGCTTTTTTACATTg                                                                    <  2:631665/141‑1 (MQ=11)                                   aaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTg                                                                    <  2:912486/141‑1 (MQ=32)                                   aaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTg                                                                    <  1:581103/141‑1 (MQ=32)                                   aaGTTAAACCAGAGCTAGGATTTGTATTAATGGCACTTAATCTAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTg                                                                    <  2:903339/141‑1 (MQ=12)                                    aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                                   <  2:59378/141‑1 (MQ=32)                                    aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                                   <  2:81160/141‑1 (MQ=32)                                    aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                                   >  2:289039/1‑141 (MQ=32)                                     gTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGcc                                                                  <  1:639295/141‑1 (MQ=32)                                              gagCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCTAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACtt                                                         <  2:294790/141‑1 (MQ=17)                                              gagCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAATAACtt                                                         >  1:30901/1‑141 (MQ=17)                                              gagCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAAAtt                                                         >  1:340771/1‑141 (MQ=17)                                                gCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATAAGCTTTTTTACATTGACTAAGAACTTaa                                                       >  2:249624/1‑141 (MQ=17)                                                 cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATCATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAAt                                                      <  1:475822/141‑1 (MQ=17)                                                   aGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGt                                                    >  2:55069/1‑141 (MQ=32)                                                                   gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTTCCTAAGAACTTAATTTCTCACCCTATTCGttt                                    >  2:301059/1‑141 (MQ=255)                                                                      cTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAGGAACTTAATGTCCCAGCCTATTCGTTTGat                                 >  1:345905/1‑140 (MQ=255)                                                                           tataAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTTAatggtt                            >  2:782755/1‑137 (MQ=255)                                                                           tataAGGAAAATAGCAGCTCAACGAGCTATACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAattatt                            >  1:594473/1‑141 (MQ=255)                                                                            ataAGGAAAATAGCAGCTCAACGAGCTGTACATTATAACATACATATCACAAAGGCTGATTTCCATCAAATAATTAATAGACATAAGCTTTTTTCCATTTCCAAAGACATTACAGTCCTAGCCTATTCGTTTTAACTAttt                           >  1:414029/1‑141 (MQ=14)                                                                              aaGGAAAATAGCAGCTCAACGAGGTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTaa                         >  2:659007/1‑141 (MQ=255)                                                                                 gAAAATAGCAGCTGAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAAttt                      <  2:56285/141‑1 (MQ=255)                                                                                        gcagcTCAACGAGCTGTACATTATAGACTAGATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTAttt               >  2:846304/1‑141 (MQ=255)                                                                                        gcagcTCAACGAGCTGTACATTATAAAATAGACAGCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACtt               >  2:846356/1‑141 (MQ=255)                                                                                        gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACtt               >  2:66746/1‑141 (MQ=255)                                                                                         cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTAAATTATTTAATTTTTTACttt              >  1:580456/1‑141 (MQ=255)                                                                                           gcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCGGCTTATTCGTTTGAATTATTTAATTTTTTACTTTgt            >  1:262194/1‑140 (MQ=255)                                                                                           gcTAAACGAGCTGTACATTATAAAATACATATCACAAAAGCTGATTTCCATCAAATAAGAAATAGAAATAAGCTATTTTACATTGCCTAAAAACTTAATGACACAGCATATTCGTTTGAATTATTTACTTTTTTACttgta            >  2:402838/1‑138 (MQ=17)                                                                                             tCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGaaa          <  1:66955/141‑1 (MQ=255)                                                                                             ccAACGCGATGTACATTATAAAACACATATCAAATAAGCGGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGaaa          <  1:859317/140‑1 (MQ=18)                                                                                                 cGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGaa      >  1:651653/1‑141 (MQ=255)                                                                                                  gAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAGTTATTTAATTTTTTACTTTGAAAGGatt     >  1:243452/1‑139 (MQ=255)                                                                                                     cTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGAATGtt  >  2:65048/1‑141 (MQ=255)                                                                                                       |                                                                                                                                           GGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGAATGTT  >  USA300TCH1516_ALE/1426926‑1427166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.