New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	27 (0.960)	9 (0.460) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	9/180	NT	32.6%	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

ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGT  >  USA300TCH1516_ALE/1998138‑1998391                                                                                                                                              |                                                                                                                  aCTGATTACGAGTCAGTTGCTCTACCAATTGAGCTAGGCGGGCCAGATGTAAGAAAGAGT‑ATACAGAAATGACGGGTACGAACCGCCGACCCTCTGCTTGTAATGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                   <  1:339967/141‑1 (MQ=11) aCTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAAAAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                   >  1:54636/1‑141 (MQ=25)   tgcttACAAGTCAGTTGCTCTACCAATTTAGCTAGGCCGGCAATATGTAAGACTAAATGGTGGAG‑AATGACGGCTTCGAACCCACGACCCTCTGCTTGTAAGGCAGATGCTCTCACAGCTGCGCTAATGCTCCCATTCaaa                                                                                                                 >  2:116998/4‑141 (MQ=11)        aCAAGTCAGTTGCTCTACCAATTGAGCTCGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGCTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGCGCTAATTCTCCGATTCACAACttc                                                                                                            >  2:282345/1‑139 (MQ=11)        aCAAGTCAGTTGCTCTACCAATTGAGCTAGGACGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCGCCCCGCTGAGCTAATTATCCGAATTAAAACTGc                                                                                                            >  2:172395/1‑141 (MQ=14)          aaGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCt                                                                                                          >  1:134719/1‑141 (MQ=255)          aaGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCt                                                                                                          <  1:240263/141‑1 (MQ=255)             tCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                       <  1:225388/141‑1 (MQ=255)                gTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATCCTCCGATTTAAAACTGCCTGGCagc                                                                                                    >  2:255243/1‑139 (MQ=255)                   gCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGtt                                                                                                 >  2:87672/1‑141 (MQ=255)                    cgctcccAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                <  1:202463/136‑1 (MQ=255)                              tGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCg                                                                                      >  1:330883/1‑141 (MQ=255)                                   tAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                 <  1:149411/141‑1 (MQ=255)                                   tAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCGCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                 <  2:68782/141‑1 (MQ=255)                                           cAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAAGTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCg                                                                         <  2:148473/141‑1 (MQ=255)                                                         aaaTGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTCAGTTCGACTACCATCGACGc                                                           >  2:54079/1‑141 (MQ=255)                                                          aaTGGTGGAG‑AAGGACGGGTTCGAACCGCCGACCCTCTTCTTGTAAGGCAGATGCTCGCCCAGCTGAGCTAATGCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCt                                                          <  2:149719/141‑1 (MQ=255)                                                           aTGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTa                                                         >  2:316120/1‑141 (MQ=255)                                                             ggtggAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGAGGAACGTAAGTTCGACTACCATCGACGCTAAg                                                       <  1:50440/141‑1 (MQ=255)                                                              gtggAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAgg                                                      >  2:105858/1‑141 (MQ=255)                                                              gtggAG‑AATGACGGGTTCGAAACATCTATGCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAATTTCGACTACCATCAACGCTACgg                                                      >  2:108195/1‑141 (MQ=14)                                                                   g‑aATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                 >  2:97224/1‑141 (MQ=255)                                                                         aCGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCACCGACGCTACGGAGCTTAACtt                                            >  2:104776/1‑141 (MQ=255)                                                                             gTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgt                                        <  1:87672/141‑1 (MQ=255)                                                                                cGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                     <  1:296534/141‑1 (MQ=255)                                                                                         gACCCTCTGCTTGTAATGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATCGCCTCTATGGAGCTTAACTTCTGTGTTCGGCATggg                            <  1:269368/141‑1 (MQ=14)                                                                                           cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATgtcaa                          >  2:100632/1‑137 (MQ=255)                                                                                               ctGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAACGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATCGGAACAga                      >  2:174397/1‑140 (MQ=255)                                                                                                     gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                <  1:219789/141‑1 (MQ=255)                                                                                                     gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                <  1:174880/141‑1 (MQ=255)                                                                                                      tAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc               <  2:134719/141‑1 (MQ=255)                                                                                                                  tctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTTGAATATCTTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg   >  1:49412/1‑141 (MQ=14)                                                                                                                   ctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGt  >  1:187834/1‑141 (MQ=255)                                                                                                                                              |                                                                                                                  ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAG‑AATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGT  >  USA300TCH1516_ALE/1998138‑1998391

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.