New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 319232	206 (1.010)	24 (0.160) +TCATAATAAAATGCATATC	11/122	NT	12.9%	coding (368/405 nt)	USA300TCH1516_00272	hypothetical protein
	?	USA300TCH1516_ALE	= 2432264	219 (1.080)					intergenic (+611/+36)	birA_2/USA300HOU_RS12525	Bifunctional ligase/repressor BirA/hypothetical protein

GAGTGAATCCTAATACTGATGCGTTAATTGAATCTTTATTTATTCAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/319184‑319232 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTTTTGATATGCATTTTATTATGAAACTGAATAAATAAAGAT  <  USA300TCH1516_ALE/2432264‑2432182                                                  |||||||||||||||||||                                                                                    GAGTGAATCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATTATAAAATGCATATCAAAAAAGCTGATTTCTATTAATT                                                              <  1:3334770/91‑1      AATCCTACTACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTG                                                         <  2:3513332/91‑1       ATCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGA                                                        <  1:2098103/91‑1       ATCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGA                                                        <  1:2560949/91‑1       ATCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGA                                                        <  1:3140838/91‑1       ATCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGA                                                        <  1:1217485/91‑1        TCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGAT                                                       <  2:1107953/91‑1        TCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGAT                                                       <  2:397984/91‑1        TCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGAT                                                       <  2:395092/91‑1        TCCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGAT                                                       <  1:3170852/91‑1         CCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATA                                                      <  1:1643214/91‑1         CCTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATA                                                      <  1:3936839/91‑1          CTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAG                                                     <  2:70904/91‑1          CTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAG                                                     <  1:3818525/91‑1          CTAATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATAACAAAAAAGCTGATTTCTATTAATTATTTGATAG                                                     <  2:220633/91‑1            AATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAA                                                   <  2:1032009/91‑1            AATACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAAGGCATATAAAAAAAGCTGATTTCTATTAATTATTTGATAGAA                                                   <  2:1031922/91‑1              TACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATCAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT                                                 <  1:3949273/91‑1              TACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT                                                 <  2:2829172/91‑1              TACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT                                                 <  1:40588/91‑1              TACTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT                                                 <  1:156950/91‑1                CTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCA                                               <  2:2663037/91‑1                CTGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCA                                               <  1:1585516/91‑1                 TGATGCGCTAATTGAATCTTTATTTATTCAGTTTCATAATAAAATGCATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAG                                              <  1:2443849/91‑1                                                             TGCATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTGATATGCATTTTTTTATGAAACTGAATAAATAAAGAT  >  2:3680247/1‑91                                                  |||||||||||||||||||                                                                                    GAGTGAATCCTAATACTGATGCGTTAATTGAATCTTTATTTATTCAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/319184‑319232 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCAGCTTTTTTGATATGCATTTTATTATGAAACTGAATAAATAAAGAT  <  USA300TCH1516_ALE/2432264‑2432182

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.