New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	35 (0.780)	30 (0.980) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	24/178	NT	55.5%	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

CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  USA300TCH1516_ALE/1998139‑1998416                                                                                                                                            |                                                                                                                                           cTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTGCTTCTCCGCTTTa                                                                                                                                            >  2:129797/1‑140 (MQ=255)   ttttACAGGCCAGTTGCTCTACCAATTGAGCTAGGCGGGCAATATGTAAGAATAAATGGTGGAGAATGGCGGGTTCGAACCGCCGAGCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaa                                                                                                                                          <  2:297333/138‑1 (MQ=11)     ttACACGGCAGTTGCTCTACCAATTGAGCTAGGCATGGAATATGTAAGAATAAATGGTCGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAAc                                                                                                                                        <  1:51228/140‑1 (MQ=14)          aGTCAGGTGCTCTACGACGTGAGGTAGGCCGGCAATATGGAAGGATAAATGGTGGCGATTGATTGGTTCGAACCGCCGACCGCCTGCTTGCAAGGCAGAGGCTCTGCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCt                                                                                                                                   <  2:367403/140‑1 (MQ=14)                    tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            <  1:53363/137‑1 (MQ=255)                    tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            >  2:53363/1‑137 (MQ=255)                    tccaCCAATGGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                         <  1:343502/137‑1 (MQ=255)                         ccaTTGAGCTAGCCCGGCAATATGTAAGAATAAATGGTGGAGAATGACAGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATTCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActc                                                                                                                    <  2:513219/138‑1 (MQ=255)                            ttGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCCGCTGAGCTCCTTCTCCGATGTCAAACTGCCTGGCAACGTTCTACTCTaa                                                                                                                 >  1:203925/1‑139 (MQ=14)                               aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAACTGAGCTAATACTCCGATCTAAAACTGCCTGGCAACGCTCTACTATAGCgg                                                                                                              >  2:448166/1‑140 (MQ=17)                                   aGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCACCGACACGCTGCTTGTAAGGCGGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                          >  1:391197/1‑140 (MQ=255)                                    ggCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTCAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGt                                                                                                         >  1:32203/1‑140 (MQ=255)                                        ggCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGt                                                                                                     >  1:517567/1‑140 (MQ=255)                                             tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCACAGGTGATACGATTCTCTGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                >  1:266012/1‑140 (MQ=17)                                               tgggaGAATAAATGGGGGAGTATGACGGGTTCGAACCGCCGACCCGCTGCTGGTGAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACGGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTa                                                                                              <  2:140967/136‑1 (MQ=14)                                               tGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTGGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCGCAGACCTACTCTAGCGGAACGTAACTTAGGCTa                                                                                              >  2:305955/1‑140 (MQ=17)                                                gTAAGAATATATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                             <  2:311837/140‑1 (MQ=255)                                                        aaaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGGACGTAAGTCCGACTACCATCGACg                                                                                     >  1:507664/1‑140 (MQ=255)                                                        aaaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACg                                                                                     >  1:67793/1‑140 (MQ=255)                                                         aagggtggAGACGGACGGGCTCGCACCGCCGACCGTCTGCTTGTAAGGCAGAGGCTCTCCCAGCTGAGCTAATTCTCGGATTTAACACTTCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGc                                                                                    <  2:363958/137‑1 (MQ=14)                                                             gttgagaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAg                                                                                <  2:472192/137‑1 (MQ=255)                                                             gtggATGATGACGGTTTCGACCCGCCGACCCTCTTCTTGTAAGGCAGATGCTCTCCCAGCTGTGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAg                                                                                <  2:45557/140‑1 (MQ=14)                                                               ggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGa                                                                              >  1:351655/1‑140 (MQ=255)                                                                     tGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGGCAAGGAGCttcg                                                                        >  2:31224/1‑138 (MQ=255)                                                                     tGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTaa                                                                        >  1:3300/1‑140 (MQ=255)                                                                         ggggTCGACCCGCCGCCCGTCTGCTTGTAAGGCAGTTGCTCCGCCGCCTGACCTAATTCTCCGATTTAACACTTCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTc                                                                    <  1:240516/140‑1 (MQ=14)                                                                         gggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGCCGCTACGATGCGTAACtgc                                                                    >  1:323713/1‑138 (MQ=17)                                                                                    ttcgtaccTCTGGTTGTGAGGCTGTTGCTCCCCCAGCTGAGCTAATTCTCCTCTTTAAAATTGCCTGGCAACGTTGTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCa                                                         <  2:292110/134‑1 (MQ=14)                                                                                    gccgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTTAGGTGCTTATCTTCTGTGTTCGGCa                                                         >  1:179309/1‑140 (MQ=255)                                                                                           ctctGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAc                                                  <  2:3300/140‑1 (MQ=255)                                                                                               gCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgt                                              >  1:262397/1‑140 (MQ=255)                                                                                                     aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGCCATGGGAACAGgtcggcga                                        >  2:114464/1‑134 (MQ=255)                                                                                                       ggCGGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAGCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                      <  2:238713/140‑1 (MQ=255)                                                                                                       ggCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                      >  1:544605/1‑140 (MQ=255)                                                                                                       ggCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACGGCCTGGCAACGTGCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                      <  2:55638/140‑1 (MQ=255)                                                                                                       cgCAGATGCTCTCCCAGCTCAGCTAATTCCCCACTTTAAAACTGCCTGTCAACATTCTACTCTATCGGAACGTAAGTTCGACTACCATCGACGCTAATGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                      <  1:387418/139‑1 (MQ=14)                                                                                                        gCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGACCTTAACTTCTGTGTTCGGCACGGGAACAGGCGTGAcatcc                                     >  1:12353/1‑140 (MQ=255)                                                                                                            aTGCTCTCCCTGCTGAGCTAATTCGCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                 <  1:440635/140‑1 (MQ=255)                                                                                                            aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCCTGCATGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                 <  2:377060/140‑1 (MQ=255)                                                                                                              gCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCta                               >  1:409495/1‑140 (MQ=255)                                                                                                               ctctCCCAGCTGAGCTAATTCTCCGAGTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGGTTAACTCCTGTGTTCCGCATGGGAACAGGAGTGACCTCATTGCtat                              >  2:233095/1‑140 (MQ=17)                                                                                                                         ttgtcTAATTCTCCGATTTATATCTGCTTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTACGGAGCCTAACTTTTGTGTTCGGCATTGGAACTGGTGTGACCTCCTTGCTATAGTCACCAGa                    <  2:96197/136‑1 (MQ=11)                                                                                                                                        aTTTACAACTGCCTGGCTACTGTCTACTCTAGCTGGACGTAAGCTCGACTACCATCGACGCTGAGGAGCTTAACTTCTGTGTTTGGCATGGTAACAGTTGTGACCTCCTTGCTATAGTCATCAGACATATGAATGTAAtt     <  2:75875/140‑1 (MQ=11)                                                                                                                                        aTTTAAATCTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAtt     <  1:437352/140‑1 (MQ=21)                                                                                                                                        aTTTAAAACTGCGTGGAAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAtt     <  1:178882/140‑1 (MQ=255)                                                                                                                                         tgtAAAAGTGCCTGGCAACGTTCTAGCCTAGTGGAAGGTAAGTTCGCCTACCATCGACGGTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAttt    <  2:373746/138‑1 (MQ=11)                                                                                                                                           tAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTGCGGACCGTCACATCTGTGTTCAGCATGGGACCAGGAGTGGCCTCCTTGCTATAGTCCACAGCCATATGACTGTCATCtat  >  2:346936/1‑140 (MQ=11)                                                                                                                                            |                                                                                                                                           CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  USA300TCH1516_ALE/1998139‑1998416

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.