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	7.0%	intergenic (‑750/+222)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	= 1912404	53 (0.710)					coding (526/609 nt)	USA300HOU_RS15290	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAATTGATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGATT  >  USA300TCH1516_ALE/1912264‑1912544                                                                                                                                             |                                                                                                                                             aaaTTGATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAAc                                                                                                                                              >  1:788145/1‑141 (MQ=35)   aTTGATGTAGTGCCTGTGTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGa                                                                                                                                            <  2:291661/141‑1 (MQ=21)       aTGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTg                                                                                                                                        >  1:291192/1‑141 (MQ=35)       aTGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTg                                                                                                                                        >  1:344253/1‑141 (MQ=35)         gTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTa                                                                                                                                      >  1:651637/1‑141 (MQ=35)          tAGAGCCTGTTTTTGGATATGTGGTGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTAc                                                                                                                                     >  2:655403/1‑141 (MQ=255)            gagCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACAt                                                                                                                                   >  2:629124/1‑141 (MQ=35)             ggCCTGTTTTTGGATTGACGAAGGCTATTTTGGGTTCAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACAtt                                                                                                                                  <  2:429843/140‑1 (MQ=255)             cgCCTTTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACCCGACCGTCCGTTCGAGGAATAAATAAAGTTACACGATAGCTAGTTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCGCAACGAGCTGTACAtt                                                                                                                                  <  1:457629/140‑1 (MQ=11)                  gTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATaaa                                                                                                                             <  2:898264/141‑1 (MQ=35)                               tGAAGGCTAGGGTGGGTTGAACTCGAACGTGAGCTAGAGGAATAAAGAAAGGGAAACGAGAGCTAGGTTGTGTATTACTGGCACTTAAAATAAGGAGGGTAGTAGCGCAACGAGCTGTACATTATAAACTACATATCaaca                                                                                                                >  2:278810/1‑139 (MQ=2)                                 aaGGGTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                              <  2:439584/141‑1 (MQ=25)                                 aaGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                              <  1:537016/141‑1 (MQ=35)                                 aaGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                              <  2:170658/141‑1 (MQ=34)                                         tttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGAttt                                                                                                      >  1:750700/1‑141 (MQ=35)                                          ttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATTGAACCGCAACGAGCTGTACATTGTAAAATACATATCAAAAAAGCTGATTTc                                                                                                     >  1:434059/1‑141 (MQ=11)                                          ttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTgtgttc                                                                                                     >  2:642753/1‑136 (MQ=25)                                            gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                   <  2:508609/141‑1 (MQ=34)                                            gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                   <  1:520968/141‑1 (MQ=35)                                            gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                   <  1:233923/141‑1 (MQ=35)                                            gggTTTAACTCAAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                   <  1:924015/141‑1 (MQ=21)                                            ggatttAACTCAAACGTCAGTTCGAGTAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                   <  2:262840/138‑1 (MQ=255)                                                 tAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCaaa                                                                                              >  1:517143/1‑141 (MQ=34)                                                 tAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCaaa                                                                                              >  1:303357/1‑141 (MQ=34)                                                 tAAATCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCGAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATAAATAAAAAAAAAGCTGATTTCTATCaaa                                                                                              <  2:745275/141‑1 (MQ=11)                                                  aaCTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaat                                                                                             <  2:59438/141‑1 (MQ=32)                                                  aaCTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaat                                                                                             <  1:810375/141‑1 (MQ=33)                                                    cTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaataa                                                                                           >  2:731630/1‑141 (MQ=32)                                                    cTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaataa                                                                                           >  2:698758/1‑141 (MQ=32)                                                                                        gagaGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAAc                                                       >  2:522696/1‑141 (MQ=11)                                                                                             cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGCACGTAAt                                                  >  2:840271/1‑141 (MQ=14)                                                                                             cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAAt                                                  >  1:705657/1‑141 (MQ=32)                                                                                              tAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAAACAGCTTTTTTGCATTACCTAAGAACTTACTg                                                 >  2:270396/1‑141 (MQ=255)                                                                                                   tttGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCa                                            >  2:367467/1‑141 (MQ=32)                                                                                                         ttAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAACTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCt                                      >  2:454513/1‑141 (MQ=17)                                                                                                           aaTGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATAAACTAATTAATAGAAATCAGCTTTTTTACACTGCCTAAGAACTTAATGTCCCAAGCCCTGa                                    <  1:629124/141‑1 (MQ=12)                                                                                                               gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGATCTTAATGTCCCAAGCCCTGACAAt                                <  1:590003/141‑1 (MQ=21)                                                                                                               gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAAt                                >  1:789969/1‑141 (MQ=34)                                                                                                                 aCTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTGAATGTCCCAAGCCCTGACAATTc                              >  2:188551/1‑141 (MQ=25)                                                                                                                  cTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGCACTTAATGTCCCAAGCCCTGACAATTCa                             >  1:71780/1‑141 (MQ=37)                                                                                                                   ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCAt                            >  1:140622/1‑141 (MQ=38)                                                                                                                   ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCAt                            >  1:488833/1‑141 (MQ=38)                                                                                                                    tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                           >  1:243593/1‑141 (MQ=38)                                                                                                                    tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                           >  1:568240/1‑141 (MQ=38)                                                                                                                    tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                           >  1:604725/1‑141 (MQ=38)                                                                                                                      atatAAGGAAAATAGCGGCTCAACGAGCTGTACATTATGAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTa                         >  1:513534/1‑141 (MQ=255)                                                                                                                            ggAAAATAGCAGCACAACGACCTTTACATTATAAAATACATATCAAAAAAGCTGCTTTCTATCAAATAATTAATAGAAATCAGCTTCTTTACATTGTCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCttt                   <  2:604375/141‑1 (MQ=14)                                                                                                                                   agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAGTTAATAGAAATCAGCTTTTTTACATTGCCTAGGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg            >  2:476908/1‑141 (MQ=255)                                                                                                                                   agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg            >  1:116365/1‑141 (MQ=255)                                                                                                                                   agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg            >  1:802085/1‑141 (MQ=255)                                                                                                                                   agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg            >  1:754935/1‑141 (MQ=255)                                                                                                                                    gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGt           >  1:110609/1‑141 (MQ=255)                                                                                                                                    gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACATTTTCAGCAGt           >  1:306325/1‑141 (MQ=255)                                                                                                                                     cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt          >  2:28887/1‑141 (MQ=255)                                                                                                                                     cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt          >  1:798063/1‑141 (MQ=255)                                                                                                                                     cagcTCAACCAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt          <  2:640366/141‑1 (MQ=255)                                                                                                                                             cGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGAtt  >  1:205286/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             AAATTGATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGATT  >  USA300TCH1516_ALE/1912264‑1912544

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