New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	48 (1.060)	26 (0.830) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	19/178	NT	44.1%	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

CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  USA300TCH1516_ALE/1998139‑1998416                                                                                                                                            |                                                                                                                                           cTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                            >  1:49325/1‑140 (MQ=37) cTGAGTACAAGTCAGTTGCTCTACCAGTTGAGCTAGGCCGGCAATTTGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                            <  2:508603/140‑1 (MQ=255)   gATCACCAGTCAGTTGCTCGACCAATTGGGCTAGGCCGGCAAGATGTAAGAATAAATGGTGGAGAATGACGGGTTCGGCCCGCCGCCCCTCTGCCTGTACGGCAGACGCTCTCCCAGCTGTGCTAATTCTCCGATTTaaa                                                                                                                                          <  2:266580/140‑1 (MQ=11)       aCAAGTCAGTTGCTCTACCAATTGGGCTAGGCCGGTAATATGTAAGAATAAAAGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTg                                                                                                                                      <  1:17253/140‑1 (MQ=255)        cAAGTCAGTTGCTCTACCAATTGGGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGATCCGCCGACCCTCTGCTTGTAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGc                                                                                                                                     <  1:307748/140‑1 (MQ=255)         aaGTCAGTTGCTCTACCAATTGAGCTAGGCCCCCAATGCAATTTTCTAAATAGTGGATAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGcc                                                                                                                                    >  1:541732/1‑140 (MQ=14)               gTTGCTCGTCCAACTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCaa                                                                                                                              <  1:469736/140‑1 (MQ=255)                ttGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATTACGGGTTCGTACCGTCTACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                             <  1:168562/140‑1 (MQ=255)                tggCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                             <  2:44669/138‑1 (MQ=255)                 tGCTTTACCAATTGCGCTAGGCCTGCTATATGTAAGAATAAATGGTGGGGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            <  1:191598/140‑1 (MQ=14)                 tGCTCTGCCAATTTGGCTGGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGTCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCCGCTGAGATAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            <  1:80881/140‑1 (MQ=17)                  gCTCTACCAATTGTGCTAGGCTGGAAACATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTCAGGCAGATGTTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGt                                                                                                                           <  2:350726/140‑1 (MQ=17)                              taGCTAGGCCGGAAATATGTAAGAATAAATTGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGTTTGTAAGGGAGATGATCTCCCAGCTGAGCTAATTCTCCGATTTAAACCTGCCTGGCAACGTTCTACTCTAGCg                                                                                                               <  1:227001/139‑1 (MQ=17)                              gatcTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACAGGCTGGGAACGTTCTACTCTAGCg                                                                                                               <  1:405132/137‑1 (MQ=255)                                   aGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTACTTCGCCGATTTGAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                          >  2:315946/1‑140 (MQ=255)                                    gtccGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCCGGCAACGTTCTACTCTAACGGAACGt                                                                                                         >  2:477385/3‑140 (MQ=255)                                             tatGTAAGAATAAATGGTGGCGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCATATGCTCTCTCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCAAGCGGAACGTAAGTTCGAc                                                                                                <  1:161904/140‑1 (MQ=255)                                             tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCTGTTGCTTTCCCAGCTGAGCTAATTATCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                <  1:23173/140‑1 (MQ=255)                                             tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCACAGTTCTACTCTAGCGGAAGGTAAGttgcgc                                                                                                >  2:232371/1‑136 (MQ=255)                                              atttAAGAATTAGTGGTGGAGAATGACGGGTTTGATCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACt                                                                                               <  1:122709/137‑1 (MQ=14)                                                ggaaGAATAAATGGTGGGGAATGACGGGTTCGCACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                             <  1:314814/138‑1 (MQ=255)                                                         aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAGGTTCAACTACCATCGACGc                                                                                    >  1:62742/1‑140 (MQ=255)                                                             ttggATAATGACGTGTTCGACACGCCGACCCCCCTCTTGTAAGGCAGATCCTCTCCGCGCTGAGCTAATTCACCGATTTAAAACGTCCTTGCAACGTTCTCCTCTAGCGGAACGTAAGTTCGACTTCCATCGAGGCTAAg                                                                                <  2:129970/139‑1 (MQ=14)                                                              tggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAAATGCCTGGCAACGTTCTACCCTAGCGGAACGTAAGTTCGACTACCATCGAGGCTAAgg                                                                               >  2:110086/1‑140 (MQ=255)                                                                 agaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                            <  2:101712/140‑1 (MQ=255)                                                                  gaATGACGGGTTCGAACCGCCTATCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCt                                                                           <  2:53194/140‑1 (MQ=255)                                                                   gaTGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                          <  1:71189/139‑1 (MQ=255)                                                                   aaTGACGGGTTCGAACCGCCGACCTTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                          <  2:437373/140‑1 (MQ=255)                                                                       aCGGCTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACt                                                                      <  2:75061/140‑1 (MQ=255)                                                                        cGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACtt                                                                     >  1:355872/1‑140 (MQ=255)                                                                        cGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGATCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAGGGAGCTTAACtt                                                                     >  1:197262/1‑140 (MQ=255)                                                                                    gccgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGCCa                                                         >  2:119696/1‑140 (MQ=255)                                                                                       gccccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCGGGCAACGTTCTACTCTAGCGGGACGTAAGTGCGAGTACCCTCGCCGCTCAGGCGCTTAACTTCTGTGTACAGCATgg                                                      >  2:331886/3‑140 (MQ=14)                                                                                       gACCCTCTCCTTGGAATGCAGCTGCTCTCCCAGCTTAGCTAATTCTCCGATTTAAAACTGCCTGGCCACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATgg                                                      <  1:57541/140‑1 (MQ=14)                                                                                         cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGCTTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    >  1:62022/1‑140 (MQ=255)                                                                                         cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    >  1:203726/1‑140 (MQ=255)                                                                                            tctGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACa                                                 <  1:477972/140‑1 (MQ=255)                                                                                                 ttGTAAGGCGGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTATGTTCTACTACCTTCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                            <  1:39015/140‑1 (MQ=255)                                                                                                   gtgaGGCAGATGCTCGCCCAGCTGAGTTAATTCTCCGATTTAAGACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTCAACTTTTTTTGTCGGCATGGGAACAGGTGTGa                                          <  2:118016/137‑1 (MQ=14)                                                                                                   gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                          <  2:548675/140‑1 (MQ=255)                                                                                                    tAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGTAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                                         <  1:251220/140‑1 (MQ=255)                                                                                                     aaGGCAGATGGTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                        >  2:372660/1‑140 (MQ=255)                                                                                                        gctgATGCTCCCCCAGTGGAGCTAATTCACCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGATTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctcc                                     <  2:369005/137‑1 (MQ=14)                                                                                                        gCAGATGCTCCCCCAGCTGAGCTAATTCTCCGATTTAAACCTGCATGGCAACGTTCTGATCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGGGAcctcc                                     <  1:111960/140‑1 (MQ=14)                                                                                                            aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                 >  1:195240/1‑140 (MQ=255)                                                                                                                         tGAGCTAATTCTCCGATTTAAATCTGCCTGGCAACGTTCTACTCTGGCTGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                    <  1:103225/140‑1 (MQ=255)                                                                                                                           aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                  >  1:337219/1‑140 (MQ=255)                                                                                                                           aGCTAATCCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                  <  1:459707/140‑1 (MQ=255)                                                                                                                            gCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACat                 >  2:316175/1‑140 (MQ=255)                                                                                                                                      cGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa       >  1:545667/1‑140 (MQ=39)                                                                                                                                        aTTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAtt     >  1:60211/1‑140 (MQ=37)                                                                                                                                         tttAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAttt    >  1:155034/1‑140 (MQ=37)                                                                                                                                           tAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTAGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtat  >  2:422871/1‑140 (MQ=21)                                                                                                                                            |                                                                                                                                           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 < 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.