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

ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512759‑512620
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAA  >  USA300TCH1516_ALE/1998278‑1998406
                                                                                                                                            ||||||||||||||||||||||||||||||||||||||||                                                                                                                                 
ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTT                                                                                                                                                                          <  2:344200/141‑1
ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTT                                                                                                                                                                          >  1:139258/1‑141
     AAATAATGTTTGTAACTTATAGTTACGGTTTTTGAAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCT                                                                                                                                                                     >  1:152975/1‑141
          ATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTACATTATTATTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATATTGTCC                                                                                                                                                                >  1:95887/1‑141
           TGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTGTCTTGTCCt                                                                                                                                                               >  1:96850/1‑140
           TGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTAAACATTTTATCAACATTTAAGTCAATAAGTTTTTTTATCTTTTCtt                                                                                                                                                               >  1:102443/1‑139
             TTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCCATAACTTTTTTTATTTTTTCCATT                                                                                                                                                             >  2:264269/1‑141
               TGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTGAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTT                                                                                                                                                           >  1:200915/1‑141
                                  TTTTGGAATAAACGTGTGTTTGTTGTTATTCTGTTTTCAATGTTCATTTTTCTTACCTACAAGAATTAATTATACATTTTATCTACATTTAAGGCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTt                                                                                                                                        <  2:326384/141‑2
                                   TTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGA                                                                                                                                       >  1:160021/1‑141
                                                 TGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATTTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCT                                                                                                                         <  1:187903/141‑1
                                                   ACATTTTGTCATTGAGTTTTTAGTGTTCATTTTTCATAACGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGG                                                                                                                       <  2:176535/141‑1
                                                     ATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTATCCAAAATTTGATTAAAAAACTTCCTGTCA                                                                                                                     >  1:242396/1‑141
                                                              TTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCCAAATTTGATTAAAAAACTGCCTGGCAACGTTCTcc                                                                                                            >  1:239173/1‑139
                                                                CAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTC                                                                                                          <  1:10615/141‑1
                                                                CAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTC                                                                                                          <  1:140260/141‑1
                                                                 AGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTAATTAAAAAACTGCCTGGCACCGTTCTACTCT                                                                                                         >  1:108565/1‑141
                                                                  aTTTTAAATTTTCATGTTTCTTACCGACAAGAATTAATTAAACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTA                                                                                                        <  2:102443/140‑1
                                                                   TTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATATGATTAAAAAACTGCCTGGCAACGTTCTACTCTAn                                                                                                       >  1:293101/1‑140
                                                                          TGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACG                                                                                                <  1:39433/141‑1
                                                                           GTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTGTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGT                                                                                               <  2:290275/141‑1
                                                                            TTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTA                                                                                              >  1:239366/1‑141
                                                                                    ttTTACCTACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTTATTAATAAACTGCCTGGCAACGTTCTACTCTAGCTTAACGTAATTTCGAt                                                                                      >  2:196775/3‑140
                                                                                       TACCGACAAGGATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCACTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAC                                                                                   <  2:321504/141‑1
                                                                                          CGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAT                                                                                <  1:327178/141‑1
                                                                                               AGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACG                                                                           <  1:304586/141‑1
                                                                                                GAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGC                                                                          <  1:29088/141‑1
                                                                                                    TAATTATACATTTTATCAACATTTAAGAAAATAACTTGTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAG                                                                      <  1:168117/141‑1
                                                                                                                 tatcAACATTTAAGTCAATGACTTTTTTTATCTTGTCCATTTTATTTTTTAACTAAAATTTGATTAAAAAACTGCCTGGCAACTTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGATCTTAACTTCT                                                         >  2:311306/5‑141
                                                                                                                  atcAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTG                                                        >  1:157162/4‑141
                                                                                                                   tcAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGT                                                       <  2:239489/139‑1
                                                                                                                   tcAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGT                                                       >  1:222783/3‑141
                                                                                                                           TAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCA                                               <  1:239732/141‑1
                                                                                                                             AGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATG                                             <  1:224420/141‑1
                                                                                                                               TCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGG                                           <  1:74487/141‑1
                                                                                                                                  ATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAC                                        <  2:58493/141‑1
                                                                                                                                     ACTTTTTTTATCTTGTACATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGG                                     <  2:17868/141‑1
                                                                                                                                      tTTTTTTTATCTTGTCTATTTTATTTTTTTACCAAAATTTGATTAAAAAGCTGCCTGGCAACGTTCTACTCTAGCTGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGT                                    <  2:352393/140‑1
                                                                                                                                      CTTTTTTTATCTTGTCCATTTTATTTTATAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGT                                    <  2:323396/141‑1
                                                                                                                                             TATCTTGTCCATTTTATTTTTTAACCAAAATTTGTTTAAAAAACTGCCTGTCTACGTTCTACTCTAGCGAAACGTAATTTCGACTACCATCGATGCTAAGGTGCTTAACTTTTGTGTTCGGCATGGGAATAGTTGTTACCT                             >  2:56764/1‑141
                                                                                                                                                aTTGTCCATTTTATTTTTTAACAAAAATGTGATTAAAAAAATGCTTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCT                          <  2:122265/140‑1
                                                                                                                                                         ttcatgTTTTAACCAACATTTGATGAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGT                 <  1:157381/135‑1
                                                                                                                                                         TTTATTTTTTAACCACAATTTTAGTAAACTACTGACTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGT                 <  2:139258/141‑1
                                                                                                                                                          TTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACTTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTC                <  2:96850/141‑1
                                                                                                                                                          TTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTC                >  1:57478/1‑141
                                                                                                                                                               TTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAG           <  2:266054/141‑1
                                                                                                                                                                   AACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGAGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACAT       >  1:114621/1‑141
                                                                                                                                                                      CAAAATTTGATTAAAAAACTGCCTAGCAACGTTCGACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATG    <  2:253011/141‑1
                                                                                                                                                                        AAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAA  <  2:222783/141‑1
                                                                                                                                            ||||||||||||||||||||||||||||||||||||||||                                                                                                                                 
ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512759‑512620
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAA  >  USA300TCH1516_ALE/1998278‑1998406

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.