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.

AAATTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGAA  >  USA300TCH1516_ALE/1426882‑1427162                                                                                                                                             |                                                                                                                                             aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTGATATAAGGAAAAGAGCAGCTCAAc                                                                                                                                              >  1:717394/1‑141 (MQ=17) aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                              >  1:81160/1‑141 (MQ=32) aaaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                              <  1:64031/141‑1 (MQ=32) aaaTTTATGCGGCGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                              <  1:293753/141‑1 (MQ=12)  aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                             >  1:77811/1‑141 (MQ=32)  aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                             >  2:376821/1‑141 (MQ=32)  aaTTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACg                                                                                                                                             >  1:77557/1‑141 (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                                                                      <  2:77811/141‑1 (MQ=32)                                                                         taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                      <  1:376821/141‑1 (MQ=32)                                                                         taaataaaGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttttt                                                                      <  2:77557/141‑1 (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                                                               <  2:81160/141‑1 (MQ=32)                                                                                aGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGc                                                               <  2:59378/141‑1 (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)                                                                                                                                             |                                                                                                                                             AAATTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAGCCTATTCGTTTGAATTATTTAATTTTTTACTTTGAAAGGAA  >  USA300TCH1516_ALE/1426882‑1427162

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.