New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	44 (0.950)	25 (0.800) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	21/166	NT	45.8%	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

ACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGT  >  USA300TCH1516_ALE/1998145‑1998409                                                                                                                                      |                                                                                                                                    aCAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGAGTTCGAACTGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                     >  1:122244/1‑134 (MQ=25)    ggTCAGTTGTTCTACCTTTCGTGCTGGGCTGGTAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCTGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaaa                                                                                                                                  <  2:393651/133‑1 (MQ=11)        aGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGc                                                                                                                              >  1:552556/1‑134 (MQ=255)           tGCTCTACCAAGTGAGCTAGGCTGGTAATATGTAATAATAAATGGTGAAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTg                                                                                                                           <  1:513765/134‑1 (MQ=14)            gCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGCGAATGACGGGTTCGCACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTgaatgg                                                                                                                          >  1:578980/1‑129 (MQ=255)             ctctTCCTATTGAGCTAGGCCGGCAATCTGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                         <  2:158382/134‑1 (MQ=255)             ctctACCGATTGAGCTAAGCCGGTAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGTACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                         <  2:250745/134‑1 (MQ=255)                 aCCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCAGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                     >  2:136866/1‑134 (MQ=255)                       tGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAc                                                                                                               >  1:335562/1‑134 (MQ=255)                       tGAGATAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAc                                                                                                               <  2:508525/134‑1 (MQ=255)                         agtatggCCGGCAATAGGTAAGAATAAGTGGGGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActc                                                                                                             <  2:347910/129‑1 (MQ=17)                                ccGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTCATTCTCCGATCTAAAACTGCCTGGCAACGAGCTACTCTACCGGa                                                                                                      >  2:149183/1‑134 (MQ=17)                                ccGGCAATATGTAAGAATAAATGGTGGAGAATAACGGGTTAGAACCGCCGACCCTCTGCTTGTGAGGCAGATGCACTCGCAGCTGAGCTGATTCGCCGAGGGAAAAATGTCTGCCAACGTTCAACTGAAGCggc                                                                                                      >  2:88779/1‑133 (MQ=14)                                 cGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCCAAATACCCCATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGaa                                                                                                     >  2:588294/1‑134 (MQ=17)                                    cAATATGTAAGAATAATTGTTGGATAATAACAGGTTCGAACCGCCGAACCGCTGCGTGGAAGGCAGAGGCGCGCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGt                                                                                                  <  1:63875/134‑1 (MQ=17)                                           tAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCACCTGAGCTCATTCCCCGCTTCCCTCCCGCCTGGCCACGTTCTAATCAAGCGGAACGTAAGTTCg                                                                                           >  1:96180/1‑134 (MQ=11)                                                    aTGGTGGGGGATGACGGGTTAGATCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                  <  2:347487/134‑1 (MQ=255)                                                    aTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATCTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                  >  1:440895/1‑134 (MQ=255)                                                                 aCGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAGTCTAGCGGAACGTAAGTTTGACTACCATCGGCGCTAAGGAGc                                                                     <  2:319565/134‑1 (MQ=255)                                                                                             gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAg                                         >  2:422913/1‑134 (MQ=255)                                                                                              acaagCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAgg                                        >  2:534496/5‑134 (MQ=255)                                                                                               aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGCCGCTAAGGTGCTTCACTTCTGTGTTCGACATGGGAACAgaa                                       >  1:238726/1‑132 (MQ=17)                                                                                               aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCAGAACGTAAGTTCGACTACCAACGACGCTAAAGAGCTTAACTTCTGTGTTCGGCATGGGAACAAgt                                       >  1:3341/1‑134 (MQ=255)                                                                                                 ggCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCAAGGGAACAGgtgt                                     >  1:306064/1‑134 (MQ=255)                                                                                                  gCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGTTCGGCTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGtgtg                                    >  1:145411/1‑134 (MQ=255)                                                                                                     gATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAGAGCTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                 <  1:539105/134‑1 (MQ=255)                                                                                                        gCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTTGGCTTGAGCACATATGTGAcctcc                              >  1:537491/1‑134 (MQ=17)                                                                                                                agctcggCTATTTCTCCGTTTTAAAACGGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTATCTTCTGTGTTCGGTATGGGAACAGGTGTGACCTCCTTGCtata                      <  2:16045/128‑1 (MQ=14)                                                                                                                       cTAATTCTCCGATTCAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCa               <  2:74039/134‑1 (MQ=255)                                                                                                                         aaTTCTTCTTTTTATAACTTCCTCGCAACGTTCTACCCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGATCCTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa             <  1:93362/134‑1 (MQ=11)                                                                                                                                   tttAAAACTTCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATg   <  1:422913/134‑1 (MQ=25)                                                                                                                                    ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAGCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGt  <  2:599445/134‑1 (MQ=25)                                                                                                                                      |                                                                                                                                    ACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGT  >  USA300TCH1516_ALE/1998145‑1998409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.