New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	30 (0.950)	25 (1.150) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	18/180	NT	54.7%	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

ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998138‑1998417                                                                                                                                             |                                                                                                                                            aCTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATAGGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                             <  1:369242/141‑1 (MQ=25)   tGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaa                                                                                                                                           >  1:55039/1‑141 (MQ=38)   tGATTACAAGGCAGTTGCTCTACCAATTGAGCCAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaa                                                                                                                                           <  1:146256/141‑1 (MQ=255)             tCAGGTGCTCTACCAATTGAGCTAGGCCGGCAATATGTACGAATAAATGGTGGTGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATGTCAAACTGCCtcgg                                                                                                                                 >  2:241293/1‑138 (MQ=14)              cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCa                                                                                                                                <  1:379003/141‑1 (MQ=255)                        aCCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAct                                                                                                                      <  2:365983/141‑1 (MQ=255)                                    aGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGt                                                                                                          <  2:142079/141‑1 (MQ=255)                                               atGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCAACCATTTAAAACTGCCGCGCGACGTTCTACTCTAGCGGAACGTAAGTTCGACTa                                                                                               <  1:390933/141‑1 (MQ=17)                                                 gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                             >  1:144122/1‑141 (MQ=255)                                                       aTAAATTGTGGAGAATGACGGGCTCGAACCGCCGACCCTCTGCTTTGAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTTCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGAc                                                                                       <  1:55748/141‑1 (MQ=14)                                                         aaaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTACAACTCCCCAGCGAGGTGCTACTCTAGCGGGACGTAAGTTCGACTACCATCGACGc                                                                                     >  1:325732/1‑141 (MQ=14)                                                           aTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGTTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGGCTACCATCGACCCTa                                                                                   >  1:84013/1‑141 (MQ=255)                                                                   gaatcgcGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                           <  2:254160/135‑1 (MQ=255)                                                                   gaATGACGGGTTCGACCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                           <  2:345971/141‑1 (MQ=255)                                                                              tCGAGCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                                <  1:352413/141‑1 (MQ=255)                                                                                         aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTCAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                     >  1:333910/1‑141 (MQ=255)                                                                                                gCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtg                                              >  2:323383/1‑141 (MQ=255)                                                                                                   tctAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAATCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGtgtgc                                           <  2:112637/139‑2 (MQ=255)                                                                                                   tGTAAGGCAGATACTCTCCCAGCTGAGCTAATTTTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGATCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTGGGCATGGGGACAGGTGTGa                                           <  2:221532/141‑1 (MQ=14)                                                                                                   tGTAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTTCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                           <  2:69924/141‑1 (MQ=255)                                                                                                       aGGCAGCTGCTCTCCCAGCTGAGATAATTCTCCGATTTTCAACTGCCTGGTAAATTTCGGCTCGATCTTGACGTAAATTCCACTACCATTCTCGCTAAGGATCGTACCTTCTTTGTGCTGCATGGGAACAGGTGTGAcctc                                       <  2:190257/141‑1 (MQ=2)                                                                                                           aGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACATCGttt                                   >  1:185291/1‑140 (MQ=255)                                                                                                             aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCt                                 >  1:151203/1‑141 (MQ=255)                                                                                                              tGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAATAGGTGTGACCTCCTTGCta                                <  1:254949/141‑1 (MQ=255)                                                                                                              tGCTCCCCCAGCTGAGCTAATTCTCCGACTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCATAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCta                                <  1:223791/141‑1 (MQ=255)                                                                                                                 tctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTTGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGGCGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg                             <  2:136506/141‑1 (MQ=255)                                                                                                                          tGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGaa                    >  1:55638/1‑140 (MQ=255)                                                                                                                           gAGCTAATTCGCCGATGTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                   <  2:220398/141‑1 (MQ=255)                                                                                                                                            tAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtata  <  1:315350/141‑1 (MQ=34)                                                                                                                                            tAAAACTGCCTGGCAACGTTATACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCAAGCGAACAGGTGTGACCTCCTTCCTATAGTCACCAGACATATGAATGTAATTtata  >  2:216668/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                            ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998138‑1998417

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.