New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 1205323102 (0.780)25 (0.260)
+AGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAG		 8/218 6.1 21.8% intergenic (‑204/‑365) USA300HOU_RS15290/lspA hypothetical protein/Lipoprotein signal peptidase
?USA300TCH1516_ALE 2478252 = 141 (1.080)intergenic (+139/‑436) USA300HOU_RS12760/USA300HOU_RS12765 hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.

GTCCAATTAAGTGTAGACGATTCATGTCTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1205181‑1205323
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAAT  >  USA300TCH1516_ALE/2478252‑2478312
                                                                                                                                               ||||||||||||||||||||||||||||||||||||||                                                             
GTCCAATTAAGTGTAGACGATTCATGTCTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGgac                                                                                                >  1:359245/1‑145
                          ttTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATA                                                                      <  2:298053/146‑1
                                    TTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAC                                                            <  1:1056518/148‑1
                                       AAGTGTTTAAAAGGAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCGCCTTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGC                                                         <  2:384472/148‑1
                                       AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGCAAGCGGAGCCATTCAATACGAAGTATTGTATAAATCGAGAGCAGa                                                         >  2:1336358/1‑147
                                       AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTTGATAAATAAGGAACAGC                                                         >  2:1027259/1‑148
                                       AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAAGGAGCAGTGCCAGTCGAAAACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTGAATACGAAGTATGGTATAAATAGAGAACAGC                                                         >  2:448168/1‑148
                                        AGTATTTAAAAGTAAAATTACATGTTAATACGTCGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGGAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACccca                                                        >  1:565776/1‑144
                                         GTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAG                                                       <  2:1364502/148‑1
                                          TATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGAAAGACGCTTATACTTCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGT                                                      <  1:611783/148‑1
                                          TATTTAAAAGTAAAATTACATGTTAATACGTAGTATAAACGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGT                                                      <  1:1414034/148‑1
                                             TTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAG                                                   >  1:550521/1‑148
                                              TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAGCAGAAGTAAGA                                                  >  2:807994/1‑148
                                              TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGA                                                  >  1:923989/1‑148
                                              TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGA                                                  <  1:1187783/148‑1
                                               AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                                                 >  1:311074/1‑148
                                                AAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                                                >  1:164467/1‑148
                                                AAAGTAAAATTACATGTTAATACGAAGAATTAATGGCGAGACTCCTAAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                                                >  1:784855/1‑148
                                                    TAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTT                                            >  2:83159/1‑148
                                                      AAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTC                                          >  2:1126220/1‑148
                                                      AAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTC                                          >  1:1327535/1‑148
                                                                         AGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACT                       <  2:467276/148‑1
                                                                         AGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCAATTAGAAAATATCTTACTG                      <  1:223222/148‑1
                                                                            ATTAATGGCGAGGCTCCTGAGGGAGCAGTGGCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCT                    <  2:557511/148‑1
                                                                                agGGCGAGTCTCCTGAGGGAGCAGTGCCAGGCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGATGTTC                <  2:520650/146‑1
                                                                                              GAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAAT  <  2:1327535/148‑1
                                                                                              GAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAAT  <  1:1126220/148‑1
                                                                                                                                               ||||||||||||||||||||||||||||||||||||||                                                             
GTCCAATTAAGTGTAGACGATTCATGTCTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1205181‑1205323
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAAT  >  USA300TCH1516_ALE/2478252‑2478312

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.