New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	26 (1.050)	22 (1.240) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	19/200	0.1	54.3%	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

ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCA  >  USA300TCH1516_ALE/1998138‑1998393                                                                                                                                             |                                                                                                                    aCTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTAGAACCGCCGACCCTCTGCTTGTAAGGCAGAAGCTCTCCCAGCCGAGCTAATTCTCCGATCTa                                                                                                                     >  2:173223/1‑141 (MQ=255)   tGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAGTTCTCCGAGTTaaa                                                                                                                   >  1:227354/1‑141 (MQ=255)        aCAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGc                                                                                                              >  1:164932/1‑141 (MQ=255)          aaGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCt                                                                                                            >  1:44618/1‑141 (MQ=255)             gcAGTTGCTCTATCAATTGAGCTAGGCCGGCAATATTTACGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                         <  2:180206/140‑1 (MQ=255)               aGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCaa                                                                                                       <  1:141090/141‑1 (MQ=255)                  tGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTCAAACTGCCTGGCCACgc                                                                                                    >  2:17753/1‑140 (MQ=255)                   gCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAGGtt                                                                                                   >  1:51216/1‑141 (MQ=255)                     tctACCAATTGAGCTCGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGCGCTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATACTCTCCCAGCTCAGCTAATTCTCCCATATCAAACCACCTCGCAACGTTcc                                                                                                 >  2:14794/1‑140 (MQ=14)                     tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTCACACAATTCTCAGACGTAACACTGCCTGGCAACGTTCt                                                                                                 >  2:100728/1‑141 (MQ=14)                        aCCAGTTGGGCTAGGCCGGCGATATGTAAGCATAAATGGTGGAGAATGACGGCTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAct                                                                                              <  2:233641/141‑1 (MQ=17)                                    aGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGt                                                                                  >  2:48004/1‑141 (MQ=255)                                       ccGGCAATATGTAGGAAGAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAg                                                                               <  1:119436/141‑1 (MQ=255)                                        cGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGt                                                                              >  2:29731/1‑141 (MQ=255)                                              tatGTAAGAATAAATGGTGGAGAATGACGGGTACGAACCGACGACCCTCTGCTTGTAAGGCAGATACTCTCCCGGCTGAGCTAATTCTCCGACTTAAAACTACCTCGCCACGTTCTACTCTAGCGGAACGTAAATTCGAcc                                                                        >  2:253092/1‑140 (MQ=17)                                                   aaGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGAGTTAAAACTGCCTTTCAACGTTCTACTCTAGCGGAACGTAAGTTCAACtttcaa                                                                   >  2:267708/1‑136 (MQ=14)                                                         aaaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGc                                                             >  1:162687/1‑141 (MQ=255)                                                              gtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTCACGGAACGTAAGTTCGACTCCCATCGCCCCTCAgg                                                        >  2:74100/1‑141 (MQ=14)                                                                   gaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                   <  1:100728/141‑1 (MQ=255)                                                                       gACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACt                                               >  1:270290/1‑141 (MQ=255)                                                                                 aaCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGCGCTAATTCTCCGATTTAAAACTGCCTGGCAGCGTTCTACTCTAGCGGCGCGTAAGTTCGACTACCATCGCCGCTACGTAGCTTATCTTCTGTTTTCg                                     >  1:90160/1‑141 (MQ=14)                                                                                    cgccgcCTCTCTGCTTGTCAGGCAGAAGCTCGCCCAGCTGAGGTGATTCTCCGATTTAAAACTTCCTGGCAACGTGCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCAAAGGAGCTTAACTTCTGTGTTCGGCa                                  <  2:17209/141‑1 (MQ=14)                                                                                         aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTACGATTTAAAACTGCCTGGCAACGTTCTACTTTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                             <  1:270236/141‑1 (MQ=255)                                                                                           ccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAc                           <  2:164932/141‑1 (MQ=255)                                                                                                  ttGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGtgtg                    <  1:48004/141‑1 (MQ=255)                                                                                                   tGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                   <  1:29731/141‑1 (MQ=255)                                                                                                                    cccAGCTGAGCTAATTCTCCGATTTAAAAGTGCCTTGCAACGTTCTACTCTAGCGGAACGTAAGTTCTACAACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCa  >  2:265614/1‑141 (MQ=255)                                                                                                                    cccAGCTGAGCTAAGTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCa  <  2:78693/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                    ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCA  >  USA300TCH1516_ALE/1998138‑1998393

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.