New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	25 (0.850)	25 (1.240) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	19/180	NT	59.2%	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

AAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTA  >  USA300TCH1516_ALE/1998147‑1998415                                                                                                                                    |                                                                                                                                          aaGTCAGTTGCTCTACCAATTCAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGATCGAACCGCCGACCATCGGGTTGTAAGGCAGATGCCGTCCCAGCTGAGCTACTTCTCCGCTATAACCCTGccg                                                                                                                                  >  2:176382/1‑140 (MQ=11)    tCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTATCCGATTTAAAACTGCCTGGc                                                                                                                               <  1:40054/141‑1 (MQ=255)    tCAGTTCCCTTACCACTTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                               <  2:116630/141‑1 (MQ=255)    gcAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                               <  1:40029/140‑1 (MQ=255)    gcAGGTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                               <  1:284822/140‑1 (MQ=255)     ctgTTGCTCTACCACTTGGGCGAGGCCCGCAATTTGTAAACATAACTGTTTTAGGTTGTCGGATTCTAACCGCCGTCCCTCTGCTTCTAATGTTGATGCGCTCTCAGCTGAGCTAATACTCCGATTTAAAACTGCCTGGCa                                                                                                                              <  2:141917/139‑1 (MQ=255)     cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCa                                                                                                                              >  2:81732/1‑141 (MQ=255)          gCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGtt                                                                                                                         >  1:149189/1‑141 (MQ=255)             ctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTa                                                                                                                      <  1:306732/141‑1 (MQ=255)                 cAATTGAGCTAGGCCGGCAATATGCAAGAATAAATGGGGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTCAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActct                                                                                                                  <  2:335908/141‑1 (MQ=255)                          tAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGGTGAGCTAATTCTCCGATTTAAAACTGTCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                         <  1:238647/141‑1 (MQ=255)                               cGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGGGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGt                                                                                                    >  1:272585/1‑141 (MQ=255)                                    atatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGGGCCGCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGGACGTAAGTTCgcc                                                                                               >  2:90738/1‑139 (MQ=255)                                    atatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                               >  2:288001/1‑141 (MQ=255)                                    atatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                               >  1:307490/1‑141 (MQ=255)                                       tGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                            <  1:307681/141‑1 (MQ=255)                                       ggtcagcaTAAATGGTGGCGAATGACGTGTCCGAACCGCCGCCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                            <  2:334891/134‑1 (MQ=17)                                        gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATGTAAAACTGCCTGGCACCGTTCTACTCTAGCGAGAGGGAAGTTCGACTAcc                                                                                           >  2:189285/1‑141 (MQ=14)                                                        gcgaATGACGCGTTCCACCCGCCGACCCACTGCATGTAAGGCAACTGCTCTCCCAGCTGAGCTAATTCTCCCACTTAAAACTCCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                           <  2:133123/139‑1 (MQ=14)                                                                      cGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATCTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                             <  2:256662/141‑1 (MQ=255)                                                                                 cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGCCTACCCACGACGCTAAGGAGCTTAACCTCTGCGTTCGGCATGGGaa                                                  >  2:99140/1‑141 (MQ=14)                                                                                            tAAGGCAGATGCTCTCCCAGCTTAGCTAATTCTCCGATTTAAAATTGCCTTGTAGCGTTCTTCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                       <  2:267796/141‑1 (MQ=14)                                                                                                    aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCt                               >  1:226794/1‑141 (MQ=255)                                                                                                       ctctCCCAGCTGAGCTAATGCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCtgta                            >  1:190455/1‑141 (MQ=255)                                                                                                          tcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTc                         >  2:357349/1‑141 (MQ=255)                                                                                                                     cTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAGCTCCTTGCTATGGTGACCAGACatat              >  1:215462/1‑141 (MQ=255)                                                                                                                     cTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACatat              >  2:339965/1‑141 (MQ=255)                                                                                                                      tAATTCTCCGGTTTAAGCCTGCCCGGCAATGTTCTCCTCGAGCGGCACGTAAGTTCGACTACCAGCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATg             <  2:313617/141‑1 (MQ=11)                                                                                                                             ccGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa      <  2:26099/141‑1 (MQ=39)                                                                                                                                 tttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAGTGTAGtttc  >  1:25413/1‑140 (MQ=255)                                                                                                                                 tttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAAGGTACTTta  >  2:68444/1‑141 (MQ=25)                                                                                                                                    |                                                                                                                                          AAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTA  >  USA300TCH1516_ALE/1998147‑1998415

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.