New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 1765719 =322 (0.900)19 (0.060) 15/146 NT 6.5% intergenic (‑26/‑377) valS/tag Valine‑‑tRNA ligase/DNA‑3‑methyladenine glycosylase 1
?USA300TCH1516_ALE 1765753 = 250 (0.770)intergenic (‑60/‑343) valS/tag Valine‑‑tRNA ligase/DNA‑3‑methyladenine glycosylase 1

CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1765815‑1765719
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggatattCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  >  USA300TCH1516_ALE/1765753‑1765842
                                                                                                                                                                                           
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATG                                                                                                  <  1:1613831/91‑1
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATG                                                                                                  <  1:1613862/91‑1
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATG                                                                                                  <  1:6237810/91‑1
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATG                                                                                                  >  1:177736/1‑91
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATG                                                                                                  <  2:1804814/91‑1
 AATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGGATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGG                                                                                                 <  2:5984521/91‑1
 AATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGGATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGG                                                                                                 <  2:3280411/91‑1
 AATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGG                                                                                                 <  2:6637847/91‑1
 AATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGG                                                                                                 <  1:277060/91‑1
 AATTATGTTAAAAGAGTGAATTTGATATTAATCATACTTCTAGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGG                                                                                                 >  1:4947639/1‑91
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATGGGATGGA                                                                                                <  2:4420165/91‑1
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGA                                                                                                >  2:5998271/1‑91
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGA                                                                                                >  1:263376/1‑91
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGA                                                                                                >  1:2952977/1‑91
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGA                                                                                                >  1:1899091/1‑91
  ATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGA                                                                                                >  1:1780029/1‑91
   TTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGAT                                                                                               <  2:10720/91‑1
   TTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGAT                                                                                               <  1:4633993/91‑1
   TTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGAT                                                                                               <  2:1644166/91‑1
   TTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGAT                                                                                               >  2:6349487/1‑91
    TATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATA                                                                                              >  1:6058357/1‑91
    TATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATA                                                                                              >  1:2133212/1‑91
     ATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCATCCTATATACAAATAGGACGGATAT                                                                                             <  1:2314697/91‑1
      TGTTAAAAGAGTGAATTTGATATTATTCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            <  2:6476037/91‑1
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            <  2:5075643/91‑1
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            <  2:5358358/91‑1
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            >  1:4724985/1‑91
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            <  2:6283501/91‑1
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            >  2:6664364/1‑91
      TGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT                                                                                            >  1:1768068/1‑91
                       TGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCATCCTATATACAAATAGGACGGATATTCCGTGGTACCACCTATA                                                                           <  2:3034844/91‑1
                            TTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCATCCTATATACAAATAGGACGGATATTCCGTGGTACCACCTATATTCAA                                                                      <  1:1227522/91‑1
                                       TCTTGAATATAGGTGGTACCACGGAATATCCATCCTATATACAAATAGGACGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATT                                                           <  1:6999699/91‑1
                                                             GGAATATACGTCCTATTTGTATATAGGATGGATATTCCATGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAA                                     >  1:6721394/1‑91
                                                                    CCGTCCTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATT                              >  2:2185182/1‑91
                                                                     CGTCCTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTG                             >  1:6854022/1‑91
                                                                      GTCCTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGG                            >  1:5622441/1‑91
                                                                       TCCTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGA                           >  2:2784192/1‑91
                                                                        CCTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAA                          >  2:6323200/1‑91
                                                                         CTATTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAAT                         >  1:6070792/1‑91
                                                                            TTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAAT                      >  2:4856582/1‑91
                                                                            TTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAAT                      >  1:697355/1‑91
                                                                            TTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAAT                      >  1:3023009/1‑91
                                                                            TTTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAAT                      >  1:5371055/1‑91
                                                                             TTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATC                     >  1:2193837/1‑91
                                                                             TTGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATC                     >  2:2283138/1‑91
                                                                              TGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCA                    >  2:3283593/1‑91
                                                                              TGTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCA                    >  1:5087142/1‑91
                                                                               GTATATAGGATGGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCAT                   >  1:471539/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATTATACCAATACTAT        >  1:5072574/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  2:4111777/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  1:6011803/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        <  1:5612611/91‑1
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  1:5129802/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  1:1532329/1‑91
                                                                                          GGATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  1:1530423/1‑91
                                                                                           GATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATC       <  2:5802752/91‑1
                                                                                           GATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATC       <  1:6118675/91‑1
                                                                                           GATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATC       >  1:439548/1‑91
                                                                                            ATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCA      >  1:624697/1‑91
                                                                                            ATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCA      <  1:4634849/91‑1
                                                                                            ATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCA      <  1:1669346/91‑1
                                                                                            ATATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCA      >  2:4692689/1‑91
                                                                                             TATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCAT     <  2:6222198/91‑1
                                                                                             TATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCAT     >  2:9589/1‑91
                                                                                             TATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCAT     <  1:1794984/91‑1
                                                                                             TATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCAT     <  2:1426417/91‑1
                                                                                              ATTCCGTGGTACCCCCTATATTCAAGAAGGATGAGTAATATCAAATTCACTCTTTTAACATAATTAGAATAATCATACAAATACTATCATC    <  1:2544363/91‑1
                                                                                              ATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATC    <  1:1282041/91‑1
                                                                                              ATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATC    <  2:1338181/91‑1
                                                                                              ATTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATC    >  1:4404660/1‑91
                                                                                               TTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTGACATAATTGGAATAATCATACCAATACTATCATCG   <  2:6744806/91‑1
                                                                                               TTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCG   >  2:4503320/1‑91
                                                                                               TTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCG   <  1:6895524/91‑1
                                                                                               TTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCG   <  2:5820103/91‑1
                                                                                               TTCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCG   <  2:5819913/91‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATTATACCAATACTATCATCGT  <  2:6523482/91‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  >  1:5513294/1‑91
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  <  2:2855940/91‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  >  1:1740138/1‑91
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  >  1:1440367/1‑91
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  <  2:3654989/91‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  <  2:3655755/91‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        >  2:1492702/1‑85
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTAT        <  1:1492702/85‑1
                                                                                                TCCGTGGTACCACCTATATTCAAGAAGGATGATTAATAGCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  <  1:5801001/91‑1
                                                                                                                                                                                           
CAATTATGTTAAAAGAGTGAATTTGATATTAATCATCCTTCTTGAATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1765815‑1765719
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggatattCCGTGGTACCACCTATATTCAAGAAGGATGATTAATATCAAATTCACTCTTTTAACATAATTGGAATAATCATACCAATACTATCATCGT  >  USA300TCH1516_ALE/1765753‑1765842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.