New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1205323	62 (0.970)	3 (0.050) +AGCGAA	3/248	NT	6.3%	intergenic (‑204/‑365)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
	?	USA300TCH1516_ALE	= 1893309	32 (0.500)					intergenic (‑170/+177)	USA300TCH1516_01750/ytpA	hypothetical protein/Phospholipase YtpA

ATTTATTAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAC  >  USA300TCH1516_ALE/1893169‑1893408                                                                                                                                              |                                                                                                    atttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTGAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGc                                                                                                     >  1:112198/1‑141 (MQ=255)  tttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCg                                                                                                    >  1:323586/1‑141 (MQ=255)  tttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTACGTGCAAGTTGGGAAAAATGTCTTATTTTATCGAAGTATTGAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCg                                                                                                    <  1:337196/141‑1 (MQ=255)  tttattAAATTATAAGAAGGGACGCAACAGAGAAAATTCATTTTATTGAATTTTACATTTATGGGCAAGTTGGGAAAAATGTCTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCg                                                                                                    <  1:337513/141‑1 (MQ=11)    tattaAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCgag                                                                                                  <  1:351706/141‑1 (MQ=255)     attaAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATAGTGCATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCgaga                                                                                                 >  1:597545/1‑141 (MQ=255)       taAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTTTT‑AATGGCGAGACt                                                                                               >  1:126387/1‑141 (MQ=255)        aaaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTc                                                                                              <  1:527173/141‑1 (MQ=255)         aaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTcc                                                                                             >  2:441069/1‑141 (MQ=255)         aaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTAAATGGTAATACGTAGTATT‑AATGGCGAGACTcc                                                                                             <  2:701915/141‑1 (MQ=255)          aTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCt                                                                                            <  1:349461/141‑1 (MQ=255)               aCGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTGAATGGCttcgctttcctag                                                                                        <  1:507450‑M2/141‑14 (MQ=255)                cGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGTCGAGACTCCTGATGGa                                                                                      >  2:231178/1‑141 (MQ=255)                cGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGa                                                                                      >  1:115742/1‑141 (MQ=255)                    gggACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAg                                                                                  >  2:236768/1‑141 (MQ=255)                      gACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTg                                                                                >  2:34217/1‑141 (MQ=255)                        cccAACACAGAAAATTCATTTTATTGGATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGcc                                                                              <  2:510685/141‑1 (MQ=255)                         ccAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCa                                                                             >  2:546808/1‑141 (MQ=255)                                     aTTCATTTTATTGAATTTTGCGTTAATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGa                                                                 >  2:544455/1‑141 (MQ=255)                                       tCATTTTATTGAATTTTACATTTATGTGCAAGTGGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACCCCTGAGGGAGCAGCGCCAGGCGAAGACCGAgg                                                               <  2:184002/141‑1 (MQ=255)                                         aTTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCt                                                             >  2:69237/1‑141 (MQ=255)                                             tATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTgaga                                                         <  2:574933/141‑1 (MQ=255)                                                     tttACATTTATGTGCAAGTTGGGATAAATGTCTTATTTTTTCAAAGTTTTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCGGTGCCAGTCGGAGTCCGAGGCTGAGACGGCAccc                                                 >  1:184822/1‑141 (MQ=14)                                                     tttACATTTATGTGCAAGATGGCGTAGATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCAccc                                                 >  1:184885/1‑141 (MQ=14)                                                        aCATTTATGTGCAAGTTGGGTAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAACTTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAg                                              >  1:51595/1‑141 (MQ=255)                                                          aTTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAATTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGa                                            >  2:385039/1‑141 (MQ=255)                                                             tATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAg                                         >  1:65801/1‑141 (MQ=255)                                                               tgtgCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCg                                       <  1:34217/141‑1 (MQ=255)                                                                  gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAg                                    <  2:115742/141‑1 (MQ=255)                                                                  gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTGAATACGTAGTATT‑AATGGCGAGACTCCTGAGTGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAg                                    <  2:224360/141‑1 (MQ=255)                                                                  gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCttcgctttcctagggtgccgtctcagcctcggtcttcgactggcactgctccctcaggagtctcg                                    >  1:589907‑M2/1‑76 (MQ=255)                                                                          ggAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCaa                            >  1:60824/1‑141 (MQ=255)                                                                                aTGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAATCGAAGCCATTCAATActtc                      <  1:88650/141‑4 (MQ=25)                                                                                aTGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGGGAAGCCATTCAATACGaa                      >  2:170145/1‑141 (MQ=25)                                                                                          ttttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGtata            <  1:65546/141‑1 (MQ=35)                                                                                          ttttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGtata            <  1:364143/141‑1 (MQ=35)                                                                                            ttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATaaa          >  2:146449/1‑141 (MQ=34)                                                                                            ttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATaaa          >  1:80185/1‑141 (MQ=35)                                                                                             tCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTGAATGGCttcgctttcctagggtgccgtctcagcctcggtcttcgactggcactgctccctcagaagtctcgccatcaatactacgtattaacatgta          >  2:507450‑M2/1‑50 (MQ=255)                                                                                                 aGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATagag     >  1:357347/1‑141 (MQ=32)                                                                                                    ttttAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAATACCGAGGCTGTGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAc  >  2:667177/2‑141 (MQ=14)                                                                                                                                              |                                                                                                    ATTTATTAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATT‑AATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAC  >  USA300TCH1516_ALE/1893169‑1893408

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.