New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 2062972139 (0.760)17 (0.100) 10/226 NT 12.2% intergenic (+53/+137) pheA/sdcS P‑protein/Sodium‑dependent dicarboxylate transporter SdcS
?USA300TCH1516_ALE = 2062986 122 (0.750)intergenic (+67/+123) pheA/sdcS P‑protein/Sodium‑dependent dicarboxylate transporter SdcS

GTTCAGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2062821‑2062972
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcaaccaaggatGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTATATCG  <  USA300TCH1516_ALE/2062986‑2062847
                                                                                                                                                                                                                                                                                                    
GTTCAGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGT                                                                                                                                                         >  1:978159/1‑141
GTTCAGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGT                                                                                                                                                         >  3:497976/1‑141
 TTCAGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTC                                                                                                                                                        <  4:622078/141‑1
    AGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAAC                                                                                                                                                     <  2:856087/141‑1
         GATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGG                                                                                                                                                >  1:123889/1‑141
         GATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGG                                                                                                                                                <  1:1443120/141‑1
         GATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGG                                                                                                                                                <  1:841248/141‑1
         GATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAACAAAGAGTCAACCAAGG                                                                                                                                                <  2:1403813/141‑1
         GATTCTGCAACTACAACCGATAGAAAGAAGGTCATTGCTATTTTAGGAACCTTAGATTTCAAAGTAGATATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAATTCAAGAGTCAACCACGG                                                                                                                                                >  4:436964/1‑141
          ATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTCGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGA                                                                                                                                               >  1:1222064/1‑141
          ATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGA                                                                                                                                               <  4:64980/141‑1
          ATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGA                                                                                                                                               <  4:292202/141‑1
          ATTCTGCAATTACAACCGATATAAAGAAAGTCATAGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGA                                                                                                                                               <  1:1610055/141‑1
           TTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGAT                                                                                                                                              >  1:1487087/1‑141
           TTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATATTAGAAACATTAGCTTTCAACGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGAT                                                                                                                                              <  3:600905/141‑1
                        ACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTT                                                                                                                                 <  1:255067/141‑1
                        ACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTT                                                                                                                                 <  1:315371/141‑1
                          aGATATAAAGAAAATCATTGCTATTTTAAAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  3:522860/140‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  2:508341/141‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  2:650164/141‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  2:309135/141‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  3:245656/141‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  4:244944/141‑1
                          CGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAA                                                                                                                               <  1:192876/141‑1
                               TAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAATCCTT                                                                                                                          <  2:613939/141‑1
                                AAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAATCCTTG                                                                                                                         <  2:380301/141‑1
                                        TCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTC                                                                                                                 <  2:852791/141‑1
                                                 TTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTT                                                                                                         >  2:94662/1‑140
                                                 TTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTT                                                                                                         <  1:94662/140‑1
                                                           CTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAACAAAAGAA‑‑AGTCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAG                                                                                            <  1:897785/141‑1
                                                                              ATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTAT                                                                                                                                    >  3:291914/1‑84
                                                                              ATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGATGGATTCCTAT                                                                                                                                    <  4:291914/84‑1
                                                                                                                                           GTCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACT              <  1:448464/141‑1
                                                                                                                                            TCAACCAAGGATGGATTCCTATTTTTATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTT             <  3:322560/141‑1
                                                                                                                                            TCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTT             <  2:611489/141‑1
                                                                                                                                            TCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTT             >  1:1344181/1‑141
                                                                                                                                            TCAACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTT             <  4:378423/141‑1
                                                                                                                                              AACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTC           <  1:1207854/141‑1
                                                                                                                                              AACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTC           >  3:53011/1‑141
                                                                                                                                              AACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTC           >  3:630310/1‑141
                                                                                                                                              AACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTC           >  1:969342/1‑141
                                                                                                                                               ACCAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCT          >  2:968575/1‑141
                                                                                                                                               ACCAACGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCAATTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCT          <  2:205067/141‑1
                                                                                                                                                 CAAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTT        <  1:1016692/141‑1
                                                                                                                                                 CAAGGATGGATTCCTATTTTAATCCTTGGTGGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCATTCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTT        <  3:315532/141‑1
                                                                                                                                                  AAGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTA       <  1:1640288/141‑1
                                                                                                                                                   AGGATGGATTCCTATTTTAATCCTTGGTTGGCTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTAT      <  1:1038316/141‑1
                                                                                                                                                   AGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTAT      <  2:1069367/141‑1
                                                                                                                                                   AGGATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTAT      >  4:497976/1‑141
                                                                                                                                                     GATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTACGGTTTCTAAAATAGCAATGACTTTCTTTATAT    <  3:519418/141‑1
                                                                                                                                                     GATGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTATAT    <  1:703423/141‑1
                                                                                                                                                       TGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTATATCG  >  1:684598/1‑141
                                                                                                                                                       TGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTATATCG  >  2:1304698/1‑141
                                                                                                                                                                                                                                                                                                    
GTTCAGGCTGATTCTGCAATTACAACCGATATAAAGAAAGTCATTGCTATTTTAGAAACCTTAGATTTCAAAGTAGAAATGATTGGTGCTTTTAATTAAACTTTATTTTCTAGGTTCTACAATTTAAATAAAATAAAGAGTCAACCAAGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2062821‑2062972
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcaaccaaggatGGATTCCTATTTTAATCCTTGGTTGACTCTTTATTTTATTTAAATTGTAGAACCTAGAAAATAAAGTTTAATTAAAAGCACCAATCATTTCTACTTTGAAATCTAAGGTTTCTAAAATAGCAATGACTTTCTTTATATCG  <  USA300TCH1516_ALE/2062986‑2062847

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