New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	39 (1.310)	23 (1.120) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	20/180	NT	46.1%	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

AGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  USA300TCH1516_ALE/1998148‑1998416                                                                                                                                   |                                                                                                                                            aGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTg                                                                                                                                  <  1:19359/141‑1 (MQ=255)        tGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGACCCGCCGACCCTCTGCTTGTACGGCAGATGCTCTCCCAGCTGGGCTAATTCTCCGGTTTCAACCGGC‑CTGACaaagc                                                                                                                           >  2:196567/1‑138 (MQ=11)         gCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATTACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTCAGCTAATTCTCCGATTTAAAACTCC‑CTGGCACCGtt                                                                                                                          >  2:24380/1‑141 (MQ=255)                 aaTTGAGACAGGCCGGCAATATGGAAGAATAATTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCCCCCAGCTGAGCTAATTCCCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTa                                                                                                                  <  1:72954/141‑1 (MQ=17)                    tGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCCCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCg                                                                                                               >  1:339634/1‑141 (MQ=255)                      aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCCCTCCCAGCTGAGCTAATTCTCCGAGTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGa                                                                                                             >  2:8443/1‑141 (MQ=255)                        cTAGGCCGGCAATATGTTAGCATAAATGGTGGAGAGTGACGGGTTCGAAGCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTGCGATTTGTGA‑TGCTCTAGCAACGTTCTACTCTAGGGGatg                                                                                                           >  2:241949/1‑139 (MQ=11)                        cTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAAc                                                                                                           >  1:164047/1‑141 (MQ=255)                         tAGGCCGGCAATACGTAAGAATAAATGGTGGAGAATGATGGGTTCGACCCGCCGACCCTCTGCTTGTAAGGCAGCTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACg                                                                                                          <  2:255469/141‑1 (MQ=255)                           ggCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTa                                                                                                        >  1:202533/1‑141 (MQ=255)                           ggCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTCC‑CTGGCAACGTTCTACTCTAGCGGAACGTa                                                                                                        >  1:110714/1‑141 (MQ=255)                              cGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGCACGTAAGt                                                                                                     >  1:146333/1‑141 (MQ=255)                                 cAATATGTAATAATAAATGGTGGAGAATTACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCg                                                                                                  <  2:152855/141‑1 (MQ=255)                                   atatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGAGGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                <  2:68204/141‑1 (MQ=255)                                       gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                            >  1:308274/1‑141 (MQ=255)                                                 aTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTa                                                                                  >  1:311643/1‑141 (MQ=255)                                                 aTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTa                                                                                  >  1:311670/1‑141 (MQ=255)                                                  tggtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTaa                                                                                 >  1:137449/1‑141 (MQ=255)                                                  tggtggAGAATGACGGGTCCGAACCGCCGACCCCCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTaa                                                                                 <  2:279799/141‑1 (MQ=255)                                                   ggtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTGAGTTCGACTACCATCGACGCTAAg                                                                                <  1:221869/141‑1 (MQ=255)                                                         gaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                          >  1:244945/1‑141 (MQ=255)                                                             ggcGGGTTCGGACGGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACGGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACt                                                                      <  2:95820/139‑1 (MQ=255)                                                                  gTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgt                                                                 <  2:164047/141‑1 (MQ=255)                                                                    tCGAACCGCCGCCCCTCTGCTGGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTGTCCGATTTAAAACTGC‑CTTGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                               <  2:4958/141‑1 (MQ=255)                                                                       aaCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCg                                                            >  1:210818/1‑141 (MQ=255)                                                                               aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    >  1:68283/1‑141 (MQ=255)                                                                               aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    <  2:147496/141‑1 (MQ=255)                                                                                 cccctGCTTGTAAGGCAGATGCTCTCCCAGCTGGGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTCCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAc                                                  <  2:24613/138‑1 (MQ=255)                                                                                     tGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAggg                                              >  1:174669/1‑140 (MQ=255)                                                                                        ttGTAAGGCAGATGCTCTCCCAACTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGtgtg                                           <  2:342422/141‑1 (MQ=255)                                                                                         tGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTACGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                          >  1:49796/1‑141 (MQ=255)                                                                                         tGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGCCTATGTTGGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                          >  1:249592/1‑141 (MQ=17)                                                                                         tGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                          >  1:105393/1‑141 (MQ=255)                                                                                          gTAAGGCAGATGCTCTCCCAGCTGTGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                                         <  2:195483/141‑1 (MQ=255)                                                                                          gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                                         >  1:201157/1‑141 (MQ=255)                                                                                                                 gAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                  <  1:311334/141‑1 (MQ=255)                                                                                                                   gCTAATTCTCCGAGTTAAAACTGC‑CTGGCAACGGTCTACTCTAGCGGAACCTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCCCCTTGCTATAGTCACCAGACata                <  1:186780/141‑1 (MQ=255)                                                                                                                    cTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACgtat               >  2:346493/1‑141 (MQ=255)                                                                                                                    cTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACAAgccgttt               >  2:346490/1‑135 (MQ=255)                                                                                                                            ccGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa       <  1:289876/141‑1 (MQ=39)                                                                                                                              gATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATACGAATGTAAtt     <  2:105393/141‑1 (MQ=38)                                                                                                                                 ttAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGGCACCAGACATATGAATGTAATTtat  >  2:278164/1‑141 (MQ=25)                                                                                                                                   |                                                                                                                                            AGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGC‑CTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  USA300TCH1516_ALE/1998148‑1998416

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.