New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 895785 =19 (0.780)13 (0.610) 12/246 0.7 42.9% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 18 (0.840)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD

GTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAAT  >  USA300TCH1516_ALE/895647‑895901
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ttgatttaaagggaaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatta                                                                                                                    >  2:109528‑M1/139‑141 (MQ=255)
 tGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAACATCCAATGGTGCAGTTAt                                                                                                                   >  2:240681/1‑141 (MQ=255)
 tGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTAt                                                                                                                   >  2:216094/1‑141 (MQ=255)
 tGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTAt                                                                                                                   >  1:99800/1‑141 (MQ=255)
    gAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTAAATACTTCATTAATGAAAAATACAATAGTGCATTTATTcc                                                                                                                >  2:166563/1‑141 (MQ=255)
       caagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttaataatctggctaaTTATTCCTGc                                                                                                             <  2:233779‑M1/10‑1 (MQ=255)
        aagggcaaaaaaagggcataattgtgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCt                                                                                                            >  2:162875‑M1/131‑141 (MQ=255)
            gcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTTTTCGTTCTAaat                                                                                                        <  1:144085‑M1/15‑1 (MQ=255)
            gcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAaat                                                                                                        <  1:273745‑M1/15‑1 (MQ=255)
             tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaata                                                                                                       >  2:263802/1‑141 (MQ=255)
                      aaaCTTAATTGATGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAAtt                                                                                              <  2:182089/141‑1 (MQ=255)
                           aaaTTGCTGTTAAAGAAGGACATAAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                         <  2:278627/140‑1 (MQ=255)
                            aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCACTtaaataa                                                                                        >  1:137659/1‑141 (MQ=255)
                                 gaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATa                                                                                   >  1:109792‑M1/106‑141 (MQ=255)
                                  aaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgccctcggacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATAc                                                                                  >  1:108077‑M1/105‑141 (MQ=255)
                                    ttAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATAccc                                                                                >  2:159602/1‑141 (MQ=255)
                                      aaagggcaagggtatgaataataaattatattgataattgtataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                              >  1:250663‑M1/101‑141 (MQ=255)
                                             gACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaac                                                                       <  1:245014/141‑1 (MQ=255)
                                             gACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaac                                                                       <  2:233063/141‑1 (MQ=255)
                                                   atgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgctctttaatttccttgataatctgactaaTTATTTCTGCTAAATAATACCAATTATATAAAAATATCTTTTaataataactat                                                                 <  2:104031‑M1/54‑4 (MQ=255)
                                                            aaaatatattgaaaaatttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGtt                                                        >  2:182614‑M1/79‑141 (MQ=255)
                                                            aGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGGTTAAGGGGtt                                                        <  1:134871/141‑1 (MQ=255)
                                                                     aaGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTtgtg                                               >  2:235454/1‑141 (MQ=255)
                                                                     aaGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACCATTACGGGGTTATTTTtgtt                                               >  2:93066/1‑140 (MQ=255)
                                                                      gaaaattttataaatgtatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                              >  1:154091‑M1/69‑141 (MQ=255)
                                                                           tAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTg                                         >  1:214017/1‑141 (MQ=255)
                                                                                      ttACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaaaaaa                              >  2:164385/1‑141 (MQ=255)
                                                                                          tataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGc                          >  1:214967‑M1/49‑141 (MQ=255)
                                                                                           ataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGca                         >  1:63285‑M1/48‑141 (MQ=255)
                                                                                            taacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcac                        >  1:107956‑M1/47‑141 (MQ=255)
                                                                                             cTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                       <  1:165550/141‑1 (MQ=255)
                                                                                                  gATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCGGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgg                  <  2:239978/141‑1 (MQ=255)
                                                                                                        gattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACTCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAACTAAAAAAGGGCACAAAACGGGCAGt            <  2:260178‑M1/107‑1 (MQ=255)
                                                                                                            gcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGAAGTatat        <  2:70236‑M1/111‑1 (MQ=255)
                                                                                                            gcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACAACTTAAATAAAAATACTCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTatat        <  2:115592‑M1/111‑1 (MQ=255)
                                                                                                               tCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGTGGTGGGAACAACACAAATAAACATAAAAGAGGGCACAAAAGGGGCAGTATATGCa     >  1:205454/1‑141 (MQ=255)
                                                                                                                  gaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAAt  <  1:19228‑M1/117‑1 (MQ=255)
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GTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAAT  >  USA300TCH1516_ALE/895647‑895901

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.