New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	16 (0.700)	28 (1.740) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	22/198	0.0	71.1%	intergenic (+688/‑6075)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	1998278 =	NA (NA)					intergenic (‑6/+3329)	USA300TCH1516_01882/USA300TCH1516_01883	tRNA‑Val/tRNA‑Ala

CAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998151‑1998417                                                                                                                                |                                                                                                                                            cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCACTCCCAGATGAGTTAAATCTCCGATTAAAAAATACCTGGc                                                                                                                                 >  1:8465/1‑140 (MQ=14)      gCTCTCCCTATTGTGCTAGGCCGGCAATATGTAAGAATATATTGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGt                                                                                                                            <  1:1200/140‑1 (MQ=17)        tttACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTTCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                          <  2:55527/138‑1 (MQ=255)        tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                          >  1:224053/1‑140 (MQ=255)        tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                          >  2:190454/1‑140 (MQ=255)            ccAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTCAGGCAGATGCTCTCCCCGCTGAGCTACTTCTCCGATTTAAAACTGCCTGGCCACGTTCTAct                                                                                                                      >  1:28658/1‑140 (MQ=255)                                 tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                 >  1:212880/1‑140 (MQ=255)                                     tgaGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGTTCGaccacc                                                                                             >  2:262846/3‑140 (MQ=255)                                        gAATAAATGGTGAAAAATGACGGGTTCGAACCGCCGACCCTCTGCTTGCAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                          <  1:34011/140‑1 (MQ=255)                                                ggtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTaa                                                                                  <  1:190454/140‑1 (MQ=255)                                                                   gAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTGCGAGTGAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                               >  1:239067/1‑140 (MQ=255)                                                                   gAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTCCCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                               >  1:120693/1‑140 (MQ=255)                                                                     aCCGCCGACACTCTTCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCg                                                             <  2:12618/140‑1 (MQ=255)                                                                          cggcccTGTGCTTGTAAGGCAGATGCTCTCGCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGATCGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATg                                                        <  2:124968/137‑1 (MQ=255)                                                                          cgACCCTCGGCTTGTACGGCCGATGCGCTCCCACCTGAGTTAATTCTCCGATTTAAGACTGCCGGGCAACGTTCTACTCCAGCGGCACGTAAGTTCGACTACCATCGACGCTAAGGCGCTTAACTTCTGTGTTCGGCATg                                                        <  2:3936/140‑1 (MQ=14)                                                                             cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCCTGGGa                                                     >  2:253092/1‑140 (MQ=255)                                                                                   gCTTGTAAGGCAGATGCTCTCCCAGCTGCGCTAATTCTCCGATTTAAAACCGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGCCGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgt                                               <  2:224053/140‑1 (MQ=255)                                                                                                             tGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                     <  2:111415/140‑1 (MQ=255)                                                                                                             tGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                     <  1:79970/140‑1 (MQ=255)                                                                                                                      tctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATCGACGCTATGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAAt            >  1:224319/1‑140 (MQ=255)                                                                                                                           gATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAt       <  1:90887/140‑1 (MQ=38)                                                                                                                                aaaaCTGCCTGTCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtata  <  1:242738/140‑1 (MQ=18)                                                                                                                                |                                                                                                                                            CAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998151‑1998417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.