New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 517640	NA (NA)	6 (0.060)	5/284	7.7	NA	intergenic (+5708/‑1055)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	= 517643	NA (NA)					intergenic (+5711/‑1052)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
Rejected: Coverage evenness skew score above cutoff.

CATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCG  >  USA300TCH1516_ALE/517584‑517791                                                            |                                                                                                                                                     cATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGttt                                                             >  2:271895/1‑149 (MQ=11)    gtgGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTAACTAGTAGCTATTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCa                                                          <  1:596700/149‑1 (MQ=11)      ggAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATg                                                        <  1:768314/149‑1 (MQ=32)       gAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGc                                                       <  1:730464/149‑1 (MQ=32)         gCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATCTGTCTGGTGACTATAGCAAGGAGGTCACACCTGCTTCCATGCCg                                                     >  2:113021/1‑149 (MQ=17)         gCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCg                                                     >  1:1033933/1‑149 (MQ=32)               caaTACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTATTTTTCAATGTATAAATTACATTCATATTTCTTGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAAcaca                                               <  1:351732/148‑1 (MQ=255)                aaTACTAATCGATCGGAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTGTACTTACTATCTAGTTTTGAATGAATAAATTACATTCATATTTCGAGAGACTATAGCAGGGAGGTCACACCTGTTTCCATGCCGAACACAg                                              >  2:102773/1‑149 (MQ=11)                 aTACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGa                                             <  1:1003519/149‑1 (MQ=32)                 aTACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGa                                             <  1:863078/149‑1 (MQ=32)                     tAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCGGAAAACAGAAGtt                                         >  2:945879/1‑149 (MQ=17)                        tcgatcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTAACTATAGAAAGGAGGTCACACCTGTTTCCATGCAGAAAACAGAAGTAAAg                                      >  2:102942/1‑149 (MQ=11)                        tcgatcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTAAATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAGGTTAAg                                      >  2:468495/1‑149 (MQ=17)                         cgatcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGGAGTTAAGc                                     >  1:50512/1‑149 (MQ=17)                           atcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACCCGGCAGTTAAGCTc                                   >  1:35768/1‑149 (MQ=12)                           atcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGccc                                   >  2:329632/1‑147 (MQ=17)                           atcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTc                                   >  1:745328/1‑149 (MQ=32)                            acgaAGACTTAATCAAGATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTAGCGAGTTGTGAATGTATAAATTACACTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTcc                                  <  2:112283/148‑1 (MQ=11)                             cgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCt                                 <  1:792015/149‑1 (MQ=32)                                    ttAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTCGCGTc                          <  2:1025312/149‑1 (MQ=17)                                       aTCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGAt                       <  1:1098886/149‑1 (MQ=32)                                        tCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACACAAGTTAAGCTCCTTAGCGTCGATg                      >  2:106715/1‑149 (MQ=17)                                          aaaaTAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATggg                    >  1:891027/1‑148 (MQ=17)                                          aaaaTAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGt                    >  2:382330/1‑149 (MQ=32)                                          aaaaTAAATGTTGTGCGAAGCAAAATCAGTTTTACTTACTATCTAGTTTTGAATATATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGATTCCATGCCGAACACAGAAGTTAAGCTGCTTAGCGTCGATGGt                    >  1:785344/1‑149 (MQ=11)                                              taaatGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGACGGTAGtt                >  1:950818/1‑148 (MQ=17)                                                 attttgggCGAAGCAAATTCACTTTTACTTACGATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGaa             <  2:276352/142‑1 (MQ=255)                                                 atGTTTTGCGAAGCAAAATCACTTTTACTTACTCTCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACGTACGTTAAGCTCCTTAGCGTCTATGGCAGTCgcg             >  2:664058/1‑147 (MQ=11)                                                 atGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGaa             <  1:947231/149‑1 (MQ=32)                                                     tttGCGCAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGCGGTCACACCTGTTTCAATGCCGAACACAGAAGTTAAGTCCCTTAGCGGCGCTGGTAGTCGAACTTa         >  2:14253/1‑149 (MQ=11)                                                     tttGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTa         >  1:323783/1‑149 (MQ=32)                                                       tGCGAAGCAAAATCAATTTTACTTACTATCTAGTTTTGAAAGAATAAATTACATTCAAATGTCAGGTGACTATAGCAAGGATGCAACTGCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACg       <  1:223316/149‑1 (MQ=11)                                                          gAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTc    >  1:457540/1‑149 (MQ=32)                                                          aaaGCAAAATCACTTTTAATTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTc    <  2:303958/148‑1 (MQ=17)                                                            aGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCg  <  1:847705/149‑1 (MQ=32)                                                            aGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCg  <  1:78020/149‑1 (MQ=32)                                                            aGCAAAATCACTTTTACTTACTATCTAGTTCTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTGCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCg  <  2:819665/149‑1 (MQ=17)                                                            |                                                                                                                                                     CATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCG  >  USA300TCH1516_ALE/517584‑517791

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.