New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	25 (0.770)	28 (1.250) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	23/180	NT	61.9%	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

CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998139‑1998417                                                                                                                                            |                                                                                                                                            cTGATTCCAGGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaa                                                                                                                                            <  2:197318/141‑1 (MQ=25) cTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGTCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGATCTAATTCTCCGAATTaa                                                                                                                                            >  1:29110/1‑141 (MQ=255)           gTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAAATGCCTgg                                                                                                                                  >  2:35112/1‑141 (MQ=255)            tCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGc                                                                                                                                 <  1:239997/141‑1 (MQ=255)             cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCa                                                                                                                                >  1:121287/1‑141 (MQ=255)             cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCa                                                                                                                                >  1:390674/1‑141 (MQ=255)               gTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                              >  1:281560/1‑141 (MQ=255)                ttGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                             >  1:235836/1‑141 (MQ=255)                   ctctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATTGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGTCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                          <  2:373681/141‑1 (MQ=255)                         cAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActct                                                                                                                    <  2:345035/141‑1 (MQ=255)                                  tAGGACTGCAATATGTAAGAATAAATGGTGTAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                           <  2:59294/141‑1 (MQ=255)                                   aGGCCTGCAATATGTAATAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGt                                                                                                          <  2:271880/141‑1 (MQ=255)                                      gctgagatatGTAAGAATAAGTGGGGTAGAATGACGGGTTCGAACCGCAGAGCCTCTGCTTGTAAGGCAGATGCTCTCCCAGTTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAg                                                                                                       <  2:58010/135‑1 (MQ=17)                                      ccGGCAATATGTAAGAATAAATGGTGGAGAATGACGGTTTCGAACCGCCGACTCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAg                                                                                                       <  2:12577/141‑1 (MQ=255)                                            atatGTGAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                 <  2:91207/141‑1 (MQ=255)                                              atGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTa                                                                                               >  1:113441/1‑141 (MQ=255)                                               tGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                              <  1:225970/141‑1 (MQ=255)                                                gTAGGAACAAAGGGTGGGGCATGGCGGTTTCGAACCGCCGGCCCTCTGCTTGTAAGGCAGATGCTCGCCCATCGGAGCTAATTCCCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                             <  2:159688/141‑1 (MQ=14)                                                 tAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCa                                                                                            >  1:216805/1‑141 (MQ=255)                                                    gAATAAATGGTGGAGAATGACGGGTACGAACCGCCGACCCTCTGCTGGTAAGGCAGATGCTCTCCCAGCTGAGCTAATGCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCg                                                                                         >  1:324129/1‑141 (MQ=255)                                                         aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGTCAACGTTCTACTCTAGCGGAACGTAAGCTCATCAACCATACACGca                                                                                    >  2:22218/1‑140 (MQ=14)                                                         aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTACGTTCGACTACCCTCGACGCt                                                                                    >  2:31974/1‑141 (MQ=255)                                                              tggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGa                                                                               >  2:305869/1‑141 (MQ=255)                                                                         gggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCTCAGCTGATCTAATTTTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCt                                                                    <  1:303932/141‑1 (MQ=255)                                                                                      cgtcgctctTCTTTCAAGGCAGGTGCTCTCGCAGCGGAGCTAATTTTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGTACGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATgg                                                       <  2:164415/136‑1 (MQ=14)                                                                                       gACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                      <  1:369194/141‑1 (MQ=255)                                                                                         cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCCGCATGGGaa                                                    >  2:299326/1‑141 (MQ=255)                                                                                            tcatcTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCACCGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAg                                                 >  2:369774/5‑141 (MQ=255)                                                                                              ttgttGTAAGGCAGATGCTTTCCCAGGTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTCCCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgt                                               <  1:208147/138‑1 (MQ=255)                                                                                                   gTAAGGGAAATGCGCTACCAGCTGAGGTGATTGTCCGATTTAAACCTGCCTGGTAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                                          <  2:57344/141‑1 (MQ=14)                                                                                                    tAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                         <  2:297485/141‑1 (MQ=255)                                                                                                     agggCAGATGCTCTGCCAGCTGAGCCAATTCTCCGATTTACACCTGCCTGCCACCGTTCTACTCTTGCGGCACGGACGTTCGACCCCCATCGGCGCTCGGGAGCTTACCTTCTGTGTTCGGCATGGGAACAGGTGTGAcct                                        <  2:294164/139‑1 (MQ=11)                                                                                                     aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcct                                        >  1:33458/1‑141 (MQ=255)                                                                                                      aGGCAGGTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                       <  1:369057/141‑1 (MQ=255)                                                                                                      aGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                       <  1:222521/141‑1 (MQ=255)                                                                                                      aGGCAGATGCTCTACCAGCTGAGCTAATTGTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                       <  2:396780/141‑1 (MQ=255)                                                                                                          aGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCTGAACTTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTg                                   <  1:35112/141‑1 (MQ=255)                                                                                                           gATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                  <  1:95997/141‑1 (MQ=255)                                                                                                               ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTCAGTTCGACTACCATAGATGTGGGTGAACTTAACTTCTGTGTTCGCCATGGGAACAGGTGTGACCTCCTTCCttta                              >  1:170028/1‑141 (MQ=17)                                                                                                               ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTATACTCTATATGAGCGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCtata                              >  1:151987/1‑141 (MQ=17)                                                                                                               ccctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACATTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCtata                              <  1:273236/139‑1 (MQ=255)                                                                                                                tctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTTTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg                             <  2:265417/141‑1 (MQ=255)                                                                                                                  gcccAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTc                           <  2:292077/140‑1 (MQ=255)                                                                                                                       gCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAATGAGATTAACATCGATGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAg                      >  2:83624/1‑141 (MQ=17)                                                                                                                          gAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                   >  1:46942/1‑141 (MQ=255)                                                                                                                           aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTCACTTCTGTGTTCCGCATGGAAACAGGTGTGCCCTCCCGACTATAGTGACCAGACac                  >  2:382837/1‑140 (MQ=14)                                                                                                                                     ccGATTTAAATCTGCCTGGCAACTTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa        <  2:46927/141‑1 (MQ=255)                                                                                                                                           tAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGCCCTCCTTGCTATAGTCCCCAGACATATGCATGGAATTtata  >  1:164073/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  USA300TCH1516_ALE/1998139‑1998417

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.