New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	43 (0.840)	7 (0.150)	6/246	NT	14.8%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	40 (0.830)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase

TAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCG  >  USA300TCH1516_ALE/801813‑802076                                                                                                                                        |                                                                                                                                 tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGCAATTGTATCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATaaaa                                                                                                                             >  1:243477/1‑140 (MQ=255) tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAg                                                                                                                             >  1:20161/1‑141 (MQ=255) tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAg                                                                                                                             >  1:628175/1‑141 (MQ=255) tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAg                                                                                                                             >  2:255285/1‑141 (MQ=255) tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAg                                                                                                                             >  1:76613/1‑141 (MQ=255)      ttacaattggttttaaagaacaaaatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATa                                                                                                                        <  1:432014‑M2/11‑1 (MQ=255)      ttacaattggttttaaagaacaaaatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaaaataaataaata                                                                                                                        >  2:544021‑M2/131‑141 (MQ=255)          cTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACttt                                                                                                                    >  2:556984/1‑141 (MQ=255)               aTGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCtt                                                                                                               <  2:80654/141‑1 (MQ=255)                  aaCTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGCCAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCtttcg                                                                                                            >  2:241444/1‑139 (MQ=255)                  aaCTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAAAATAGAGAAAATGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAg                                                                                                            >  1:60236/1‑141 (MQ=255)                     aagaacaagatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGaaa                                                                                                         <  1:414769‑M2/26‑1 (MQ=255)                     aagaacaaaatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccacaacATAAAGAAATACTTTTTCTTTAGaaa                                                                                                         <  1:93893‑M2/26‑1 (MQ=255)                       ttATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAAtt                                                                                                       >  2:277243/1‑141 (MQ=255)                        tATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTa                                                                                                      >  1:312920/1‑141 (MQ=255)                        aacaaaatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTa                                                                                                      >  2:626230‑M2/113‑141 (MQ=255)                             cTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAAGATAACGGAAAACTTTTTCTTTAGGATTTAGTAtt                                                                                                 >  1:600136/1‑141 (MQ=21)                             cTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTCGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTAtt                                                                                                 <  1:127572/141‑1 (MQ=255)                                  acacTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCACGATGGATAGCTCTTCATCATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTa                                                                                            >  1:632091/1‑141 (MQ=18)                                       acaacaCTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTATAAATTAGTATTTCTTATGCAt                                                                                       >  2:311254/1‑141 (MQ=255)                                         aacaCTATATTGGCAGTAGTTGACTGCGGGGCCCAAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATGAAGAAAGACTTGTTCTTTAGAAATGAGTATTTCTTATGCATGa                                                                                     >  2:327035/1‑141 (MQ=18)                                           cacTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACCGGCAATGCAAGTTGGGGTGTGACCCAACACAACGAAATACTTTTTCTTTAGAAATTAGTACTTATTATGCATGatt                                                                                   >  2:193455/1‑139 (MQ=18)                                            acTAGAGTGGCAGTAGTTGACTGCGGGGCGCCAACATAGATAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAgtg                                                                                  <  2:55569/141‑1 (MQ=255)                                                 atTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCTAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACt                                                                             <  2:379879/141‑1 (MQ=255)                                                  ttGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTc                                                                            >  1:524129/1‑141 (MQ=255)                                                              gACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGACCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCatat                                                                <  1:333742/141‑1 (MQ=255)                                                              aaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCatat                                                                >  1:11567‑M2/75‑141 (MQ=255)                                                                  gCGGGGCACCAACATAGCGGTGTTGGAACGCATAATTATACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATAttttt                                                            <  2:132274/141‑1 (MQ=18)                                                                   cGGGGCCCCAACATAGAGGAGGTGGAATGCCAATTTCTATAGACAATGCAAGTTGGGGTGGGCCCTAACATAAAGAAATTCTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTTACGCATGCATTCATATTTTTa                                                           <  2:393605/141‑1 (MQ=14)                                                                    ggggCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATCTCTTATGCATCCCGGTAACTCATTCATGCACATTTTTac                                                          >  1:621874/1‑140 (MQ=14)                                                                     gggCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGCTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAACTAGTATTTCTTATGCACGAGTGTAACTCATCCACTCATATTTTTacg                                                         >  2:254754/1‑139 (MQ=17)                                                                      ggggccAACAGAGAGGAGTGGGAACGCCAATTTCTAGAGAGAATGCAAGTTGGGGTGGGCACCAACAGAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGt                                                        <  2:632294/137‑1 (MQ=17)                                                                         ctcAATATAGAGAAATTGGAACGCCAATTTCTAGAGACAGTGCAAGTTGGAGTGGGCCCCAACATAAAGAAATACTTTTTCTGTAGCTTTTATTATTTTTTATGCGTGAGTGTAACTCATGCATTCATATTTTTAAGTaca                                                     <  2:263161/139‑1 (MQ=18)                                                                         cccAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTaca                                                     <  1:562595/141‑1 (MQ=255)                                                                          ccAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTacac                                                    <  1:246907/141‑1 (MQ=255)                                                                            aaCATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAt                                                  <  2:20161/141‑1 (MQ=255)                                                                                      aaTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGAc                                        <  1:64010/141‑1 (MQ=255)                                                                                           gAACGACAATTTCTACAGACAATGCAAGTTGGGGTTGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATg                                   <  1:352573/141‑1 (MQ=255)                                                                                                ccAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATaaa                              <  1:277243/141‑1 (MQ=255)                                                                                                 cAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATCAAg                             >  1:160926/1‑141 (MQ=255)                                                                                                   aTTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGaa                           <  1:255285/141‑1 (MQ=255)                                                                                                          cAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATCAAGAATCGCTAc                    >  2:515407/1‑141 (MQ=255)                                                                                                          cAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATGAGCTGTGACTAATCATACAGAATCGCTAc                    >  2:534679/1‑141 (MQ=255)                                                                                                            aaCAATGCAAGTTGGGGTGTGCCACAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACAt                  <  1:210423/140‑1 (MQ=255)                                                                                                                aTGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaatc              <  1:311254/141‑1 (MQ=255)                                                                                                                 tGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaatca             >  1:480393/1‑141 (MQ=255)                                                                                                                      gTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCAt        <  1:241444/141‑1 (MQ=255)                                                                                                                          cgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGt    <  1:626230‑M2/127‑1 (MQ=255)                                                                                                                            gTGGGCCCCAACATAAAGAAATACTTTGTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCg  <  2:632091/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                 TAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCG  >  USA300TCH1516_ALE/801813‑802076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.