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.

CATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACG  >  USA300TCH1516_ALE/517584‑517786                                                         |                                                                                                                                                   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)                                                         |                                                                                                                                                   CATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACG  >  USA300TCH1516_ALE/517584‑517786

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.