New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	57 (1.000)	34 (0.850) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	30/188	0.2	46.0%	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

TACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAT  >  USA300TCH1516_ALE/1998144‑1998412                                                                                                                                       |                                                                                                                                       tACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCTAGTTTAGCTAATTCTCCGATTTa                                                                                                                                        <  1:586124/135‑1 (MQ=255) aaCAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCTTTTTa                                                                                                                                        <  1:458669/134‑1 (MQ=255)    taGTCAGTTGCTCTACCGATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGTTAATTCTCCGATTTaaaa                                                                                                                                     <  1:174208/134‑1 (MQ=255)     aGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTTCCAGCTGAGTTAATTCTCCGATTTAAAAc                                                                                                                                    <  1:14585/135‑1 (MQ=255)         aGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACGGcc                                                                                                                                <  1:307447/135‑1 (MQ=255)                    cAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                     >  1:439889/1‑135 (MQ=255)                    cAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGATTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                     >  2:451104/1‑135 (MQ=255)                            cTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAg                                                                                                             >  1:653057/1‑135 (MQ=255)                              agaccGGCAAAATGTAAGAATGAATGGTGAAGATTGCCGTTTTCGAACCGCCGACCCTCTTCTTGTAAGGCGTATGCTCGCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCGTGGCAACCTTCTACTCTAGCg                                                                                                           <  2:99778/132‑1 (MQ=17)                              aGGCCGGCAATATGTAAGAATAAATGGTGGATAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCg                                                                                                           >  1:667968/1‑135 (MQ=255)                               ggCCGGCAAGATGTGAGAATCAATAGTGGAGAATGACGGCTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCgg                                                                                                          >  1:306965/1‑135 (MQ=17)                                gCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTAGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTGGCggc                                                                                                         >  2:234078/1‑134 (MQ=255)                                 ccGGCAATAGGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGaa                                                                                                        >  2:352972/1‑135 (MQ=255)                                        tatGTAAGAATAAATGGTGGAAAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGt                                                                                                 >  1:549672/1‑135 (MQ=255)                                         atGTAACAAGAAATGGTGGAGAATGACGGGTTCCAACCGCCGACCCTCTGTTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACCTTCTACTCTAGCGGAACGTAAGtt                                                                                                <  2:166075/135‑1 (MQ=17)                                                   aactggtggAGAATGACGGGTTCGAACCGCCGCCCCCCTGCTTATAAGGCAGATGCTCTCCCAGCTGAGCTACTACTCCTATTTAAAACTTCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAt                                                                                      <  2:586996/132‑1 (MQ=14)                                                   aaaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTATTCTAGTGGATCGTAAGTTCGACTACCAt                                                                                      <  1:556689/135‑1 (MQ=255)                                                   aaaTGGGGGAGAATGACGGGTTCGAACCGCCGACCCTCCGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGACCGTAAGTTCGACTACCAt                                                                                      <  2:284393/135‑1 (MQ=255)                                                    aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                     <  2:676008/135‑1 (MQ=255)                                                          ggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCt                                                                               >  1:444506/1‑135 (MQ=255)                                                          ggAAAATGACGGGTTCGAACAGCCGACCCTCTGCTGGTAAGGCAGATGCTCTCGCAGCTGACCTAATTCTCCGATTTAAAACTGCCTGGCACCGTTCTACTCTAGCGGTACGAAAGTTCGACTACCATCGACGCt                                                                               >  2:353284/1‑135 (MQ=14)                                                             gaATGACCGGTTCGAACCGCCGACCCTCTGCTTGTAAGGACGATGCCGCCGCAGCGGAGCGAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAg                                                                            >  2:430713/1‑135 (MQ=17)                                                              aaTGACGGGTTCGAACAGCCAACCCTATGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAgg                                                                           >  1:493904/1‑135 (MQ=255)                                                                  aCGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCt                                                                       <  2:601180/135‑1 (MQ=255)                                                                  aCGGGTTCGAACCGCCGAATCTCTCCTATAAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCt                                                                       >  1:272767/1‑135 (MQ=17)                                                                           aaCCGCCGACGCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtg                                                              >  2:670377/1‑135 (MQ=255)                                                                             ccgccgACCCTCTGCTTGTAAGCCAAATGCTCTCCCAGCTGAGCTCATTCTTTGATTTAAAACTGCCTGGCAACGTTCCACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgtg                                                            <  2:380741/135‑1 (MQ=14)                                                                               gccgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTAAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                          >  1:25742/1‑135 (MQ=255)                                                                                 cgACCCTCTGCTTGTAAGGCAGATGATCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCg                                                        >  1:491676/1‑135 (MQ=255)                                                                                 cgACCCTCTGCTTGTAAGGCAAATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCg                                                        >  1:509341/1‑135 (MQ=255)                                                                                   aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGc                                                      <  2:348671/135‑1 (MQ=255)                                                                                        ctGCTTGTAAGGCAGATACTCTCCCAGCTAAGCTAATTCTCCGATTTAAAACTGCCCGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                 >  1:6136/1‑135 (MQ=255)                                                                                        ctGCTTGTAAGGCAAATACACACCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                 >  1:145861/1‑135 (MQ=255)                                                                                         tGCTTGTAATGCAGATGCTCTCCCAACTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                >  1:624990/1‑135 (MQ=255)                                                                                         tGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                >  1:34125/1‑135 (MQ=255)                                                                                         tGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAACTTTCCGATCTAAAACTGCCGGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGAATGGGa                                                >  2:43024/1‑135 (MQ=14)                                                                                         tGCTTGTAAGGCAGATACTCTCCCAGCTGAACTAATTCTCCGAATTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAGGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                >  1:116691/1‑135 (MQ=255)                                                                                          gCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGaa                                               <  2:25742/135‑1 (MQ=255)                                                                                           cTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAc                                              <  1:339063/135‑1 (MQ=255)                                                                                              gTAAGGCAGATGCTTTCCCATCTGAGCTAATTCTCCGATTTAAAACTGCCGGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGCCGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAgg                                           <  2:253086/135‑1 (MQ=255)                                                                                              gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAgg                                           <  2:484456/135‑1 (MQ=255)                                                                                               tAAGGCAGGTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTTCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTTTGTGTTCGGCATGGGAACAGgt                                          <  1:227109/135‑1 (MQ=255)                                                                                                gaGGCAGCTGCTCTCCCAGCTGAGCTAATTATCCTATTTAAAACTGCCTGGCAATGTTCTTCGCTAGCGGAACGTAAGTTCGACTACCTTCGTCGTTTTGGATTTTATCTTCTGTGTTTGGCATGGGAACAGgtg                                         <  1:21292/134‑1 (MQ=14)                                                                                                aaGGCAGATGCCCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtg                                         <  2:437010/135‑1 (MQ=255)                                                                                                 aGGCCGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACCCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGTTTAACTTCTTTGTTTGGTATGGGAACAGgtgt                                        <  1:25755/135‑1 (MQ=14)                                                                                                   gctgtggCTGTCCCACCTGAGTGAATTCTTCGGTTTAAAACTGCCTGGCTACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTTTGTTCGGTATGGGAACAGGTGTGa                                      <  1:249165/129‑1 (MQ=14)                                                                                                     aGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAGTACTTAGGAGGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                    >  1:147608/1‑135 (MQ=17)                                                                                                     aGATGCTCTCCCAGCTGAGCTAATTCTCCAATTTAAAACAACCTAGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                    >  1:45388/1‑135 (MQ=255)                                                                                                       aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                  <  2:190095/135‑1 (MQ=255)                                                                                                          ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCtt                               >  2:355270/1‑135 (MQ=255)                                                                                                          ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTATAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCtt                               >  2:672155/1‑135 (MQ=255)                                                                                                           tctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTg                              <  2:594712/135‑1 (MQ=255)                                                                                                           tctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTg                              <  2:124936/135‑1 (MQ=255)                                                                                                            ctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGTATGGGAACAGGTGTGACCTCCTTGc                             <  1:527604/135‑1 (MQ=255)                                                                                                            ctcCCAGCTGAGCTAACTCTCCAATTTAAAACTGCCTGGCAACGTCCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCGAATGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                             <  2:587380/135‑1 (MQ=14)                                                                                                             tcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCt                            <  1:435290/135‑1 (MQ=255)                                                                                                              cccAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCta                           <  2:555959/135‑1 (MQ=255)                                                                                                                 aGCTGAGCTCATTCTCCGATTTAAAAACGCCTGGCAACGTTCTCCTCTAGCGGAACGTAAGTTCGACTACCATTGACGCTAAGGAGCTTAACTTCGGTGTTTGGGAGGGGAACAGGTGTGACCGCCTTGCTATAg                        <  2:43759/135‑1 (MQ=14)                                                                                                                 aGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCTACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg                        <  2:165592/135‑1 (MQ=255)                                                                                                                      tgCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCAcc                   <  1:271657/134‑1 (MQ=255)                                                                                                                      aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTTCTTGCTATAGTCAcc                   <  1:138972/135‑1 (MQ=255)                                                                                                                       gCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTGGCGGAACGTAAGTTCGACTACCATCGCCGCTAAGGAACTTAACTTCTGTGTTCCGCATGGGAACGGGTGTGACCTCCTTGCTATAGTCGCCa                  >  2:490423/1‑135 (MQ=14)                                                                                                                          aaTTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTATGGAAAGGTGGTTATAGTCACCAGAc               <  2:433938/135‑1 (MQ=14)                                                                                                                           aTTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa              <  2:493904/135‑1 (MQ=255)                                                                                                                              ctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAATAGGTGTGACCTTCTTTTTATAGTCACCAGACatat           <  1:519846/135‑1 (MQ=255)                                                                                                                              ctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACatat           <  2:145861/135‑1 (MQ=255)                                                                                                                              ctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACatat           <  2:6136/135‑1 (MQ=255)                                                                                                                               tcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGTTGTGAACTTTTTACGAAATGCACCAGACATATg          <  1:670377/135‑1 (MQ=14)                                                                                                                               tcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATg          <  2:495411/135‑1 (MQ=40)                                                                                                                                     ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTa    >  2:657396/1‑135 (MQ=35)                                                                                                                                     ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCGTGCTATAGTCACCAGACATATGAATGTa    <  2:389388/135‑1 (MQ=25)                                                                                                                                       aaaaCTGCCTGGCAACGTTCTACTCTAGCGAAACAAAAGTTAGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAt  >  1:223653/1‑135 (MQ=255)                                                                                                                                       |                                                                                                                                       TACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAT  >  USA300TCH1516_ALE/1998144‑1998412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.