New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1427019	55 (0.700)	4 (0.050)	3/268	9.3	8.0%	intergenic (‑750/+222)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	= 1427022	39 (0.520)					intergenic (‑753/+219)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAAATTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAA  >  USA300TCH1516_ALE/1426881‑1427158                                                                                                                                           |                                                                                                                                            aaaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCaa                                                                                                                                           >  2:722926/1‑141 (MQ=32)  aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTGATATAAGGAAAAGAGCAGCTCAAc                                                                                                                                          >  1:717394/1‑141 (MQ=17)  aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                          <  1:64031/141‑1 (MQ=32)  aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                          >  1:81160/1‑141 (MQ=32)  aaaTTTATGCGGCGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                          <  1:293753/141‑1 (MQ=12)   aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                         >  1:77557/1‑141 (MQ=32)   aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                         >  1:77811/1‑141 (MQ=32)   aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                         >  2:376821/1‑141 (MQ=32)     tttATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAg                                                                                                                                       <  1:588058/141‑1 (MQ=32)      ttATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGc                                                                                                                                      <  1:83551/141‑1 (MQ=31)       tATGTAGTGCTTGTTTTTGGATTTATGAAGACTATTTTGGGTTTTCCTCTTATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  1:298770/141‑1 (MQ=11)       tATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAATTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  2:161073/141‑1 (MQ=11)       tATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  1:580029/141‑1 (MQ=11)       tATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  1:718256/141‑1 (MQ=11)       tATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  2:336250/141‑1 (MQ=11)       tATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATCAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  1:633488/141‑1 (MQ=11)       tATGGAGATCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCt                                                                                                                                     <  2:337595/141‑1 (MQ=11)                                              ggTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCAt                                                                                              >  1:483095/1‑141 (MQ=32)                                                               aGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGaaa                                                                             <  2:597127/141‑1 (MQ=32)                                                                gTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAAt                                                                            <  2:520698/141‑1 (MQ=32)                                                                          taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                  <  1:376821/141‑1 (MQ=32)                                                                          taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                  <  2:77557/141‑1 (MQ=32)                                                                          taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                  <  2:77811/141‑1 (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                                                            <  1:581103/141‑1 (MQ=32)                                                                                aaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTg                                                            <  2:912486/141‑1 (MQ=32)                                                                                aaGTTAAACCAGAGCTAGGATTTGTATTAATGGCACTTAATCTAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTg                                                            <  2:903339/141‑1 (MQ=12)                                                                                 aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                           <  2:59378/141‑1 (MQ=32)                                                                                 aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                           >  2:289039/1‑141 (MQ=32)                                                                                 aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                           <  2:81160/141‑1 (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)                                                                                                                                           |                                                                                                                                            AAAATTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAA  >  USA300TCH1516_ALE/1426881‑1427158

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.