New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2080726 =	47 (1.020)	4 (0.100)	4/234	NT	9.0%	intergenic (‑194/‑347)	USA300HOU_RS10505/aspC	hypothetical protein/Aspartate aminotransferase
	?	USA300TCH1516_ALE	2080759 =	39 (0.940)					intergenic (‑227/‑314)	USA300HOU_RS10505/aspC	hypothetical protein/Aspartate aminotransferase

GTGTAATGATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2080878‑2080726 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagacttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  >  USA300TCH1516_ALE/2080759‑2080897                                                                                                                                                                                                                                                                                                      GTGTAATGATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACC                                                                                                                                                         <  2:328321/141‑1      ATGATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACT                                                                                                                                                    <  1:710183/141‑1         ATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGG                                                                                                                                                 >  2:199135/1‑141         ATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGG                                                                                                                                                 >  2:199130/1‑141            TGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGGGGT                                                                                                                                              >  1:376534/1‑141             GGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGGGGTT                                                                                                                                             >  1:362607/1‑141                GGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGGGGTTttg                                                                                                                                          >  1:652369/1‑138                              ATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGAT                                                                                                                            <  1:619380/141‑1                                  ctaTTATTNCAGGTGGCTTACTAATTATTTTTCGTCTTTGGTTNGAACTGAAATGGAAAAATAAAANATGATCCTACACACATAAATAACCCCAAGTCTGGTAACGGCGGCTTTGGGGTTATTTATGTGTGTAGGATCATT                                                                                                                        <  2:175666/138‑1                                                                                                                               AAGTCTGCTGGTACCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCA                           >  1:304818/1‑141                                                                                                                                      CTGGTACCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAAGTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACT                    >  2:155479/1‑141                                                                                                                                              AGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCC            >  1:162110/1‑141                                                                                                                                                ACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGT          <  2:14312/141‑1                                                                                                                                                    GGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCATTTCTAACCAATGTCGTAATATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCTCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGA      <  1:25870/141‑1                                                                                                                                                        TTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  <  1:55629/141‑1                                                                                                                                                        TTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  <  2:84982/141‑1                                                                                                                                                        TTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACCACACCTCCGTTCGACTAA  <  1:427588/141‑1                                                                                                                                                                                                                                                                                                      GTGTAATGATGTGGTGGCAAGAAGGGATGATGACACTTATTACAGGTGGCTTACTAATTATTTTTCGACTTTGGTTAGAACTGAAATGGAAAAATAAAAAATGATCCTACACACATAAATAACCCCAAGTCTGCTGGTACCAGACTTGGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2080878‑2080726 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagacttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  >  USA300TCH1516_ALE/2080759‑2080897

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