New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	729254 =	47 (1.020)	3 (0.070)	3/236	NT	6.8%	intergenic (+55/‑96)	USA300HOU_RS03535/aes	hypothetical protein/Acetyl esterase
	?	USA300TCH1516_ALE	729295 =	40 (0.950)					intergenic (+96/‑55)	USA300HOU_RS03535/aes	hypothetical protein/Acetyl esterase

GGATATGTAGGCTTATTTATTGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTAT  >  USA300TCH1516_ALE/729116‑729393                                                                                                                                           |                                                                                                                                            tgtttcagatgaaatgctaacaatacactgattacagttataaaaagcgcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataaaa                                                                                                                                           <  1:68977‑M1/3‑1 (MQ=255)  gtttcagatgaaatgctaacaatacactgattacagttataaaaagcgcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataaaaa                                                                                                                                          >  1:407426‑M1/138‑141 (MQ=255)   tttcagatgaaatgctaacaatacactgattacagttataaaaagcgcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataAAAAg                                                                                                                                         <  1:238115‑M1/5‑1 (MQ=255)    tatGTAGGCTTATTTATTGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATTCTGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGc                                                                                                                                        <  1:553080/141‑1 (MQ=255)        gatgaaatgctaacaatacactgattacagttataaaaagcgcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataAAAAGCAAtt                                                                                                                                    <  2:222640‑M1/10‑1 (MQ=255)           gCTTATTTATTGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGt                                                                                                                                 >  1:293368/1‑141 (MQ=255)                 ttattGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTAc                                                                                                                           <  1:497878/141‑1 (MQ=255)                    ttGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCAATTTGTTTTAACCTTATAATCAATTCGTCTCTActct                                                                                                                        >  1:153496/1‑141 (MQ=255)                      gtagtaGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTa                                                                                                                      <  1:362890/141‑1 (MQ=255)                          tagCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCgg                                                                                                                  >  2:10693/1‑141 (MQ=255)                           agCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCggg                                                                                                                 <  1:29134/141‑1 (MQ=255)                            gCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTGTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGc                                                                                                                >  1:13986/1‑141 (MQ=255)                                ttacagttataaaaagcgcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataAAAAGCAATTCGTCTCTACTCTTATCGGGCGAAt                                                                                                            >  1:750174‑M1/108‑141 (MQ=255)                                tAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAAt                                                                                                            >  1:437916/1‑141 (MQ=255)                                  attattAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTg                                                                                                          <  1:211594/141‑1 (MQ=255)                                   ttattaAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGc                                                                                                         <  1:763856/141‑1 (MQ=255)                                      ttaAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCttt                                                                                                      <  2:257901/141‑1 (MQ=255)                                       taAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCACTTCGTCTCTACTCTTATCGGGCGAATTGCtttt                                                                                                     >  2:332172/1‑141 (MQ=255)                                       taAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCtttt                                                                                                     <  1:652962/141‑1 (MQ=255)                                       taAATATTGCAAAAGTAAAAATGAGGATCAAAAACATATTGCTTAATATACTATGAGGGATATCAGCAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCtttt                                                                                                     <  1:196925/141‑1 (MQ=255)                                               tCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTAtattta                                                                                             >  1:692819/1‑141 (MQ=255)                                                cAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTAtatttat                                                                                            <  1:286323/141‑1 (MQ=255)                                                 gcagttatcatcgtccatttattatctttattcattacatcgtacctctctatttgttagacgctcatattaatagactgaataaatataAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTAtatttatt                                                                                           >  2:144276‑M1/91‑141 (MQ=255)                                                     gTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAGACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGt                                                                                       >  1:595921/1‑141 (MQ=255)                                                          aaTGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTAtt                                                                                  >  2:148721/1‑141 (MQ=255)                                                          aaTGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTAtt                                                                                  <  2:227597/141‑1 (MQ=255)                                                              cGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAata                                                                              <  1:464917/141‑1 (MQ=255)                                                                gATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATg                                                                            >  1:275644/1‑141 (MQ=255)                                                                gATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATg                                                                            <  1:27826/141‑1 (MQ=255)                                                                 aTAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATGAATATGa                                                                           <  1:623286/141‑1 (MQ=255)                                                                  tAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAg                                                                          <  1:340460/141‑1 (MQ=255)                                                                        aCATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTa                                                                    <  1:376020/141‑1 (MQ=255)                                                                          atatTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAAc                                                                  <  1:164932/141‑1 (MQ=255)                                                                          atatTGCGTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAAc                                                                  <  1:593741/141‑1 (MQ=255)                                                                              tGCTTAATCTCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTCACAGCAAATCGTCTCTACTCTTCTCGGGCGCCTTGCATTTTATATTTCTCCAGTCTATTAATATGAGCGTCTAACAAAt                                                              >  1:549180/1‑141 (MQ=255)                                                                                      atCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGt                                                      <  2:95147/141‑1 (MQ=255)                                                                                         atatGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACg                                                   >  2:177343/1‑141 (MQ=255)                                                                                              aGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTa                                              <  2:10298/141‑1 (MQ=255)                                                                                               gggATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTaa                                             >  1:602445/1‑141 (MQ=255)                                                                                                ggATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAAt                                            <  2:332849/141‑1 (MQ=255)                                                                                                ggATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGCACGATGTAAt                                            >  1:339486/1‑141 (MQ=255)                                                                                                  atatCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGa                                          >  1:73580/1‑141 (MQ=255)                                                                                                   tatCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGaa                                         >  1:53200/1‑141 (MQ=255)                                                                                                        gttagacgctcatattaatagactgaataaatataAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGTGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAg                                    >  1:568981‑M1/36‑141 (MQ=255)                                                                                                             tttACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATCCCGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGataat                               <  1:214298/141‑1 (MQ=255)                                                                                                              ttACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGataata                              >  2:303225/1‑141 (MQ=255)                                                                                                                aCAATTGAATCACTTTGTTTTAACCTTAGAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATaaa                            >  1:91252/1‑141 (MQ=255)                                                                                                                         tCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACgatg                   <  1:139252/141‑1 (MQ=255)                                                                                                                              ttGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAAc              <  1:445751/141‑1 (MQ=255)                                                                                                                                 ttttAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTgc           <  1:41197/141‑1 (MQ=255)                                                                                                                                  tttAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTgcg          >  2:87580/1‑141 (MQ=255)                                                                                                                                   ttAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTgcgc         <  2:191034/141‑1 (MQ=255)                                                                                                                                    tAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCt        <  1:539495/141‑1 (MQ=255)                                                                                                                                    tAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCt        >  1:93156/1‑141 (MQ=255)                                                                                                                                      aCCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCttt      <  2:178276/141‑1 (MQ=255)                                                                                                                                          tAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTtat  >  1:393280/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                            GGATATGTAGGCTTATTTATTGTAGTAGCTGTAATTATTAAATATTTCAAACGTAAAAATGCGGATAAAAAACATATTGCTTAATATCATATGAGGGATATCCGAAACTTTACAATTGAATCACTTTGTTTTAACCTTAAAAGCAATTCGTCTCTACTCTTATCGGGCGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTAT  >  USA300TCH1516_ALE/729116‑729393

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