New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	37094 =	41 (1.300)	3 (0.100)	3/240	NT	6.8%	intergenic (+118/‑719)	USA300HOU_RS14915/ugpQ_1	hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic
	?	USA300TCH1516_ALE	37188 =	45 (1.550)					intergenic (+212/‑625)	USA300HOU_RS14915/ugpQ_1	hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic

AACATATAAGATAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATTATA  >  USA300TCH1516_ALE/36955‑37229                                                                                                                                            |                                                                                                                                        aacgtacctcttatctgtaattttactgagaactgcttttaacaaacctcttatctgcaattttacttagaattgcttttactattcctcttattagtataatctcagtaagaatgcgtataaaaatgaaaattacaacCg                                                                                                                                        <  2:270482‑M1/2‑1 (MQ=255)         aGAAAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTa                                                                                                                                <  2:314895/141‑1 (MQ=255)                gaAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCAt                                                                                                                         >  1:212314/1‑141 (MQ=255)                       aCTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTTcc                                                                                                                  >  2:347205/1‑141 (MQ=255)                       aCTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGcc                                                                                                                  >  2:339266/1‑141 (MQ=255)                                     gtgCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCtg                                                                                                    >  2:166804/1‑140 (MQ=255)                                            atgaGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCAt                                                                                             <  1:296322/141‑1 (MQ=255)                                                gCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGATTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGAATGGCTGGGGCAGTTAGt                                                                                         >  1:123932/1‑141 (MQ=255)                                                ctcttatctgcaattttacttagaattgcttttactattcctcttattagtataatctcagtaagaatgcgtataaaaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGt                                                                                         >  2:63504‑M1/93‑141 (MQ=255)                                                 cTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATCTTTTCCGTGTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtc                                                                                        <  1:187977/141‑1 (MQ=255)                                                   tGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctc                                                                                      <  2:284244/141‑1 (MQ=255)                                                   tGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGATAGAAGTTGATTATGGCTCGAGCCATTAGtctc                                                                                      <  1:392355/141‑1 (MQ=255)                                                   tGGGACACAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctc                                                                                      <  2:221400/141‑1 (MQ=255)                                                    gggTCATAAATCATACCGCGACATTAATAAGCATATCACTAACCTGATGTTTCAAAGTTTACAGTGATATGCTTATTTTGTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctct                                                                                     <  2:13869/141‑1 (MQ=255)                                                               ccTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTa                                                                          >  1:270482/1‑141 (MQ=255)                                                                cTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTAt                                                                         >  1:117587/1‑141 (MQ=255)                                                                    cTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTccc                                                                     >  1:47164/1‑141 (MQ=255)                                                                    cTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTccc                                                                     >  2:314009/1‑141 (MQ=255)                                                                       gAAATAAATAAGCATATCACTAAACTGAGTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGTACATACTATTCCCtag                                                                  >  1:331355/1‑139 (MQ=255)                                                                                     tatCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTTCTAGTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTa                                                    <  1:109802/141‑1 (MQ=255)                                                                                                 gATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTTTGTGTCTCCTTGCCTAGGGGTATGGGTTGAGTCATCCGTCTTGCGCACAGAGGATTTCGTCATGGTGCTGCACGTACAAAATCGGTTg                                        >  2:34212/1‑141 (MQ=255)                                                                                                 gATTTTTTAAAGGTTACAGGGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTg                                        <  2:75146/141‑1 (MQ=255)                                                                                                      tttAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAtt                                   >  1:376366/1‑141 (MQ=255)                                                                                                      tttAAAGGTTACAGTGATATGCTTATTTTTTTATCTTACGAGTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAtt                                   <  1:149055/141‑1 (MQ=255)                                                                                                       ttAAAAGTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAttt                                  <  2:121708/141‑1 (MQ=255)                                                                                                           aGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAt                              >  1:23970/1‑141 (MQ=255)                                                                                                             tttACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttt                            <  1:46420/141‑1 (MQ=255)                                                                                                             taagaatgcgtataaaaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttt                            <  2:55175‑M1/110‑1 (MQ=255)                                                                                                               tACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttttt                          >  1:42534/1‑141 (MQ=255)                                                                                                                 cAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATTCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTtat                        <  1:369184/141‑1 (MQ=255)                                                                                                                  aGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTtata                       <  1:30/141‑1 (MQ=255)                                                                                                                    tGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACg                     <  1:106932/141‑1 (MQ=255)                                                                                                                    ggATATGCTTACTCTTCTAGCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACg                     <  1:148527/140‑1 (MQ=255)                                                                                                                     gATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGc                    >  1:341830/1‑141 (MQ=255)                                                                                                                     gATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGc                    <  1:79369/141‑1 (MQ=255)                                                                                                                       tatGCTTATTTTTTTATCTTACGATTTTGGACGTGCATGCCTGCCTCGGGGTATGGCTCGAGCCATTAGTCTCTCTCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCAt                  <  2:132671/141‑1 (MQ=255)                                                                                                                           cTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCtt              <  1:318880/141‑1 (MQ=255)                                                                                                                           cTTATTTTCTTATCTTACTATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCtt              <  1:155325/141‑1 (MQ=255)                                                                                                                            aaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTa             >  1:55175‑M1/17‑141 (MQ=255)                                                                                                                              aTTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACt           <  2:70962/141‑1 (MQ=255)                                                                                                                               tttttttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTg          <  1:166804/141‑1 (MQ=255)                                                                                                                                ttttttATCTTACGATTTTGTACGGGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTga         <  1:91896/141‑1 (MQ=255)                                                                                                                                   tttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGAt      >  2:277866/1‑141 (MQ=255)                                                                                                                                   tttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATAGGTTGTCATTTTCATTTTTATAAGCCTTCTTACTGAGAt      >  1:58792/1‑141 (MQ=255)                                                                                                                                      aTCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtat   <  1:314009/141‑1 (MQ=255)                                                                                                                                       tCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtata  <  2:113774/141‑1 (MQ=255)                                                                                                                                       tCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtata  >  1:236937/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                        AACATATAAGATAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATTATA  >  USA300TCH1516_ALE/36955‑37229

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.