New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 769784	151 (0.790)	10 (0.060)	8/146	NT	6.2%	coding (91/465 nt)	USA300HOU_RS03760	hypothetical protein
	?	USA300TCH1516_ALE	= 769799	165 (0.950)					coding (106/465 nt)	USA300HOU_RS03760	hypothetical protein

GGAAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/769688‑769784 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttagcaaGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  <  USA300TCH1516_ALE/769799‑769710                                                                                                                                                                                             GGAAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATAT                                                                                                  <  1:85821/91‑1  GAAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATT                                                                                                 <  1:2450114/91‑1   agATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTA                                                                                                <  2:1136340/89‑1   AAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTA                                                                                                <  2:1136471/91‑1   AAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTA                                                                                                <  1:564732/91‑1   AAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTA                                                                                                <  1:2260854/91‑1   AAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGATGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTA                                                                                                <  2:2989661/91‑1    AATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAG                                                                                               >  2:3200131/1‑91    AATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAG                                                                                               <  1:2991117/91‑1     ATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGC                                                                                              <  1:1045069/91‑1      TGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCA                                                                                             >  2:3382957/1‑91      TGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCA                                                                                             >  2:1897285/1‑91      TGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCA                                                                                             <  2:2283057/91‑1       GTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA                                                                                            >  2:1660199/1‑91       GTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA                                                                                            <  1:1364020/91‑1       GTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA                                                                                            >  1:1502290/1‑91       GTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA                                                                                            >  1:3388999/1‑91       GTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA                                                                                            >  1:2375207/1‑91                          TAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGC                                                                         <  1:499/91‑1                            AAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTA                                                                       <  1:3841520/91‑1                              AAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTCAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAAT                                                                     <  2:3480647/91‑1                                ATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATAT                                                                   <  1:1513993/91‑1                                ATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATAT                                                                   <  1:687412/91‑1                                ATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATAT                                                                   <  1:1965468/91‑1                                    ATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATATTAAT                                                               <  2:3205579/91‑1                                       TTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAA                                                            <  1:532111/91‑1                                             CTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGTTTTATGTACCTTAGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATT                                                      <  2:1575049/91‑1                                                      TGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACG                                             <  1:592869/91‑1                                                                                           TTAGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTT        >  1:1548623/1‑91                                                                                            TAGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTT       <  1:2632320/91‑1                                                                                             AGCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTT      >  2:973670/1‑91                                                                                              GCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTA     >  1:77036/1‑91                                                                                              GCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTA     >  2:2888701/1‑91                                                                                              GCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTA     <  2:3210007/91‑1                                                                                              GCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTA     >  2:550626/1‑91                                                                                              GCAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTA     <  1:1318103/91‑1                                                                                               CAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTAC    >  1:3408628/1‑91                                                                                               CAAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTAC    >  1:2343886/1‑91                                                                                                AAGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACT   <  2:432064/91‑1                                                                                                 AGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  <  1:3628546/91‑1                                                                                                 AGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  >  1:3202348/1‑91                                                                                                 AGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  >  1:2738542/1‑91                                                                                                 AGCGCATCTTCACTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  >  1:2974722/1‑91                                                                                                                                                                                             GGAAATGTGGGTAAGGGGATGACAGTAAAAAATTTATTTTTAGGCTTTGTTGCTGTAATATTAACCGTTTGTTTAATTGGTTTATTAATATTAGCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/769688‑769784 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttagcaaGCGCATCTTCATTTGTTGCTAATATTAATAAACCAATTAAACAAACGGTTAATATTACAGCAACAAAGCCTAAAAATAAATTTTTTACTG  <  USA300TCH1516_ALE/769799‑769710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.