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

GTTCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATT  >  USA300TCH1516_ALE/512485‑512760
                                                                                                                                       |                                                                                                                                            
gTTCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTAGTTGTTGAGGACACCATTATAGCTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAg                                                                                                                                         >  1:272248/1‑141 (MQ=255)
acctgttcccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttataaaataaaatggacaagataaAAAAAg                                                                                                                                         <  2:323396‑M1/6‑1 (MQ=255)
acctgttcccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttcagctagagtagaacgttgccaggcagctttttaatcaaattttggtaaaaaaataaaatagacaagataaaaaaaa                                                                                                                                         <  2:352393‑M1/6‑2 (MQ=255)
 cctgttcccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatgtacaagataaAAAAAGt                                                                                                                                        <  2:17868‑M1/7‑1 (MQ=255)
    gttcccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTAt                                                                                                                                     <  2:58493‑M1/10‑1 (MQ=255)
       cccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGa                                                                                                                                  <  1:74487‑M1/13‑1 (MQ=255)
         catgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACt                                                                                                                                <  1:224420‑M1/15‑1 (MQ=255)
           tgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTa                                                                                                                              <  1:239732‑M1/17‑1 (MQ=255)
                  aGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTta                                                                                                                       <  1:81662/141‑1 (MQ=255)
                  aGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTta                                                                                                                       >  1:111123/1‑141 (MQ=255)
                   acagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAAtgttga                                                                                                                      <  2:239489‑M1/25‑3 (MQ=255)
                   acagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAAtgttga                                                                                                                      >  1:222783‑M1/117‑139 (MQ=255)
                    cagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAatgttgat                                                                                                                     >  1:157162‑M1/116‑138 (MQ=255)
                     agaagttaagatccttagcgtcgatggtagtcgaacttacgttccgctagagtagaaagttgccaggcagttttttaatcaaattttagttaaaaaataaaatggacaagataaAAAAAGTCATTGACTTAaatgttgata                                                                                                                    >  2:311306‑M1/115‑137 (MQ=255)
                       tAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATcaa                                                                                                                  >  1:283590/1‑141 (MQ=255)
                        aaTTTGTTCTTTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAATTTGAATTACTAACGAAAATTAATTTTAAATCGTTATTTACTTAAATGTTAATaaaa                                                                                                                 <  2:368370/141‑1 (MQ=255)
                         aTTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAAt                                                                                                                >  1:313744/1‑141 (MQ=255)
                              tACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTATTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGtata                                                                                                           <  1:323871/141‑1 (MQ=255)
                                cTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATTTTAATAAAATGTAtaat                                                                                                         >  1:140746/1‑141 (MQ=255)
                                  cttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAACAAGTTATTTTCTTAAATGTTGATAAAATGTAtaatta                                                                                                       <  1:168117‑M1/40‑1 (MQ=255)
                                      gcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTc                                                                                                   <  1:29088‑M1/44‑1 (MQ=255)
                                       cgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCt                                                                                                  <  1:304586‑M1/45‑1 (MQ=255)
                                          gCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATCACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATAAACTTAAATGTAAATAAAATATATAATAAATTATTgc                                                                                               >  2:234679/1‑140 (MQ=255)
                                            atggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCg                                                                                             <  1:327178‑M1/50‑1 (MQ=255)
                                            aGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTATATGTTAATAAAATGTATAATTAATTCTTGTCg                                                                                             >  2:275223/1‑141 (MQ=255)
                                            aGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCg                                                                                             >  1:70367/1‑141 (MQ=255)
                                            aGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCg                                                                                             >  1:81435/1‑141 (MQ=255)
                                               gtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaagtggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATCCTTGTCGGTa                                                                                          <  2:321504‑M1/53‑1 (MQ=255)
                                                  atcgaaattacgttaagctagagtagaacgttgccaggcagtttattaataaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTAGgtaaaa                                                                                       >  2:196775‑M1/86‑139 (MQ=255)
                                                   aaGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaa                                                                                      >  2:231226/1‑141 (MQ=255)
                                                   aaGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaa                                                                                      <  2:111123/141‑1 (MQ=255)
                                                          tacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGaa                                                                               >  1:239366‑M1/78‑141 (MQ=255)
                                                           acgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaatacaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAAc                                                                              <  2:290275‑M1/65‑1 (MQ=255)
                                                            cgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACa                                                                             <  1:39433‑M1/66‑1 (MQ=255)
                                                                   ntagagtagaacgttgccaggcagttttttaatcatattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGaaaa                                                                      >  1:293101‑M1/69‑141 (MQ=255)
                                                                    tagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTTTAATTAATTCTTGTCGGTAAGAAACATGAAAATTtaaaat                                                                     <  2:102443‑M1/74‑2 (MQ=255)
                                                                     agagtagaacggtgccaggcagttttttaattaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACt                                                                    >  1:108565‑M1/67‑141 (MQ=255)
                                                                      gagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTg                                                                   <  1:10615‑M1/76‑1 (MQ=255)
                                                                      gagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTg                                                                   <  1:140260‑M1/76‑1 (MQ=255)
                                                                        ggagaacgttgccaggcagttttttaatcaaatttgggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGaa                                                                 >  1:239173‑M1/64‑141 (MQ=255)
                                                                               aaaaaaaaacaAATAAACATACGAAATAACTTGAAATACTAAAAAAAAAAAATTTTAAAAAGATATCAACTAAAATATTAATAAAATGTATAATTAATTAAAAAAAAAAAAAAAAATGAACATTGAAAACTGAATGACAat                                                          <  2:382754/140‑1 (MQ=255)
                                                                                 tgacaggaagttttttaatcaaattttggataaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAatat                                                        >  1:242396‑M1/55‑141 (MQ=255)
                                                                                 aacaaaacaaCTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAatat                                                        >  1:308484/1‑141 (MQ=255)
                                                                                   ccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGTTATGAAAAATGAACACTAAAAACTCAATGACAAAATGt                                                      <  2:176535‑M1/89‑1 (MQ=255)
                                                                                     aggcagttttttaatcaaattttggttaaaaaataaaatggacaaaataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCa                                                    <  1:187903‑M1/91‑1 (MQ=255)
                                                                                       acaacTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAc                                                  >  1:70047/1‑141 (MQ=255)
                                                                                             gaactTGAGAGATAACTTGAATTACTAACGAAAATTAATTGTAAAAAGTTATTGACTTAAATGGTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAGGTTAAt                                            >  1:134097/2‑141 (MQ=39)
                                                                                             caactTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAAt                                            >  2:86177/1‑141 (MQ=255)
                                                                                               actTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAAtcc                                          >  2:213660/1‑139 (MQ=255)
                                                                                                   tcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaaa                                      >  1:160021‑M1/37‑141 (MQ=255)
                                                                                                    aaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGCCTTAAATGTAGATAAAATGTATAATTAATTCTTGTAGGTAAGAAAAATGAACATTGAAAACAGAATAACAACAAACACACGTTTATTCCaaaa                                     <  2:326384‑M1/106‑1 (MQ=255)
                                                                                                       aaTAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAAc                                  >  2:103471/1‑141 (MQ=255)
                                                                                                              tGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaaaa                                                                                    <  1:2165/84‑1 (MQ=255)
                                                                                                              tGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaaaa                                                                                    >  2:2165/1‑84 (MQ=255)
                                                                                                                     atAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTa                    <  1:246278/140‑1 (MQ=255)
                                                                                                                       aaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTCAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACa                  >  1:200915‑M1/17‑141 (MQ=255)
                                                                                                                         aatggaaaaaataaAAAAAGTTATGGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACaaa                >  2:264269‑M1/15‑141 (MQ=255)
                                                                                                                           aggacaagacaaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACa              >  1:96850‑M1/13‑141 (MQ=255)
                                                                                                                           aagaaaagataaAAAAACTTATTGACTTAAATGTTGATAAAATGTTTAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACa              >  1:102443‑M1/13‑141 (MQ=255)
                                                                                                                            ggacaatataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAATAATAATGTACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACat             >  1:95887‑M1/12‑141 (MQ=255)
                                                                                                                                 agataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTTCAAAAACCGTAACTATAAGTTACAAACATTAttt        >  1:152975‑M1/7‑141 (MQ=255)
                                                                                                                                 aattTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAAGTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTAttt        <  1:312920/141‑1 (MQ=255)
                                                                                                                                   ttttAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAg      <  1:307755/141‑1 (MQ=255)
                                                                                                                                      aAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTAt   <  2:344200‑M1/140‑1 (MQ=255)
                                                                                                                                      aAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTAt   >  1:139258‑M1/2‑141 (MQ=255)
                                                                                                                                       aaaaaGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGATAAGAAAAATGAACATTGAAAAATGAATGACAGTATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTAtt  >  1:228048/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                            
GTTCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATT  >  USA300TCH1516_ALE/512485‑512760

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.