New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2080223 =	19 (0.530)	3 (0.090)	3/264	3.4	14.0%	intergenic (‑131/+133)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
	?	USA300TCH1516_ALE	= 2080217	19 (0.560)					intergenic (‑125/+139)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAATATACACAATATACACAGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGTTTTAAAC  >  USA300TCH1516_ALE/2080124‑2080347                                                                                              |                                                                                                                                   caatatacacaatatacaCAGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATAAAATGACACTACCA‑TTAATCTTGCATTGTCTAc                                                                                    <  1:366062/141‑1 (MQ=255)     atacacaatatacacaGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTc                                                                                 <  1:133695/141‑1 (MQ=255)     atacacaatatacacaGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTc                                                                                 <  1:183418/141‑1 (MQ=255)          caatatacacaGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATaa                                                                            >  1:183451/1‑141 (MQ=255)                acacaGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGa                                                                      <  1:326381/141‑1 (MQ=255)                 cacaGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTCGCATTGTCTACTTCAATAAAAAAGAc                                                                     >  2:369010/1‑141 (MQ=255)                     gTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCt                                                                 >  2:162620/1‑141 (MQ=255)                          gTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAAc                                                            <  1:236382/141‑1 (MQ=255)                          gTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAAc                                                            <  1:390699/141‑1 (MQ=255)                          gTAAATATGCATGTC‑CATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTG‑‑‑‑‑AATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGt                                                      >  1:204676/1‑141 (MQ=255)                           tAAATATGCATGTC‑CATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTG‑‑‑‑‑AATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTc                                                     >  1:381470/1‑141 (MQ=255)                              atatGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTG‑‑‑‑‑AATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCtt                                                   >  1:400954/1‑141 (MQ=255)                                   cATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCtt                                                   >  1:347600/1‑141 (MQ=255)                                   cATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCtt                                                   <  2:147279/141‑1 (MQ=255)                                       tctcATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAAt                                               <  2:19305/141‑1 (MQ=255)                                       tctcATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAAt                                               <  2:52178/141‑1 (MQ=255)                                                               aaTAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCa                       >  2:134270/1‑141 (MQ=255)                                                                     acTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATaa                 <  2:347600/141‑1 (MQ=255)                                                                              tgtattACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGtt        >  2:90431/1‑141 (MQ=255)                                                                                 attACTAGCAGTTGAATAAAATAAAATGAAATGACACGACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGTTTTa     <  1:150698/141‑1 (MQ=255)                                                                                    aCTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGTTTTAAAc  >  2:400470/1‑141 (MQ=255)                                                                                    aCTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGTTTTAAAc  >  2:31240/1‑141 (MQ=255)                                                                                              |                                                                                                                                   CAATATACACAATATACACAGTTTTGTAAATATGCATGTCTCATTATCAACCAGTCTTCAGAAATAACACTGAGTATTGTATTACTAGCAGTTGAATAAAATAAAATGAAATGACACTACCATTTAATCTTGCATTGTCTACTTCAATAAAAAAGACTGCTAAAACGAATGTCTTTAATCTCTACGTGACAACCGTAGCGTCAACATAAACAATCGTTTTAAAC  >  USA300TCH1516_ALE/2080124‑2080347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.