New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	28 (0.940)	3 (0.110)	3/246	NT	10.3%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	26 (0.920)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase

AAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATC  >  USA300TCH1516_ALE/801810‑802085                                                                                                                                           |                                                                                                                                          aaGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGAAAGTTGGGGTGGGCCCCAACATa                                                                                                                                         <  2:246767/141‑1 (MQ=255)                         tttATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAAt                                                                                                                 <  1:74492/141‑1 (MQ=255)                             tGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTGGAAATTAGt                                                                                                             >  2:262970/1‑141 (MQ=255)                                aatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTAtt                                                                                                          <  2:216013‑M2/34‑1 (MQ=255)                                   gataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtggtacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCt                                                                                                       <  2:205135‑M2/37‑1 (MQ=255)                                             acacTATATTTGCAGTAGTTTACTTCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGCTAATTTTATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTTTGCATGAg                                                                                             >  1:235013/1‑141 (MQ=14)                                               attgtatTGGCAGTAGTTGACTGCGGGGCCCAAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAgtg                                                                                           <  2:283770/137‑1 (MQ=255)                                               acTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAgtg                                                                                           <  2:76215/141‑1 (MQ=255)                                                  atatTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTTTGCATGAGTGTaa                                                                                        >  2:90467/1‑141 (MQ=255)                                                     ttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTc                                                                                     <  2:292847‑M2/55‑1 (MQ=255)                                                              gtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCa                                                                            <  1:50849/141‑1 (MQ=255)                                                              gtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCGTATGCATGAGTGTAACTCATGCATTCa                                                                            <  1:342891/141‑1 (MQ=255)                                                                 gACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCatat                                                                         >  1:237416/1‑141 (MQ=255)                                                                 gACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCatat                                                                         >  1:4007/1‑141 (MQ=255)                                                                  aCTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCTAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTTatata                                                                        >  2:210225/1‑140 (MQ=255)                                                                             ccAACATAGAGAAATTGGAACGCCAATTTCTGCAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGCAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTacac                                                             >  2:90087/1‑141 (MQ=255)                                                                             ccAACATAGAGAAATTGGAACGCCAATTTCTACAGCCAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTCTTTCTTATGCCTGAGTGTAACACATGCATTCATCTTTTTAAGTagac                                                             >  2:90071/1‑141 (MQ=17)                                                                                   tAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGc                                                       <  2:33225/141‑1 (MQ=255)                                                                                       aaaaTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCtgtg                                                   <  2:220102/140‑1 (MQ=255)                                                                                              gAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATg                                            >  1:156816/1‑141 (MQ=255)                                                                                               aaCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGa                                           >  1:155663/1‑141 (MQ=255)                                                                                               aaCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGa                                           >  1:162452/1‑141 (MQ=255)                                                                                                aCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGAt                                          >  1:142923/1‑141 (MQ=255)                                                                                                         tCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGCAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCGTTCATATTTTTAAGTACACGTTAGCTTTGACTATTGATAAAGagtgg                                 >  2:44211/1‑137 (MQ=18)                                                                                                             cAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTAc                             <  2:231017/141‑1 (MQ=255)                                                                                                             cAGACAATGCAAGTTGAGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTAc                             <  2:204826/141‑1 (MQ=255)                                                                                                               gACTATGTAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTATTATTTCTTACGCATGAGTGTAACTCATGCATTCATCTTTTTAAGTACACATTAGCTGTGACTAATGATAAAGCATCGCTACAt                           <  2:285083/141‑1 (MQ=18)                                                                                                                    tGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACAGaatca                      >  2:251421/1‑141 (MQ=255)                                                                                                                        aGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGACATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACTCATTAGCTGTGACTCATGATAAAGAATCGCTAACTAatcaatca                  >  1:28802/1‑141 (MQ=18)                                                                                                                              ggTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTACTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTc            >  1:293311/1‑141 (MQ=255)                                                                                                                                tGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGt          >  1:293361/1‑141 (MQ=255)                                                                                                                                        aacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCGTTAGTCGTTGTTTATc  >  1:308805‑M2/4‑141 (MQ=255)                                                                                                                                           |                                                                                                                                          AAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATC  >  USA300TCH1516_ALE/801810‑802085

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.