New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1205323	177 (0.950)	39 (0.210)	5/296	17.5	18.1%	intergenic (‑204/‑365)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
	?	USA300TCH1516_ALE	1205383 =	175 (0.940)					intergenic (‑264/‑305)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1205210‑1205323 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTTAATTAGAAAATATCTTACT  >  USA300TCH1516_ALE/1205383‑1205460                                                                                                                                                                                                  TATTTTTTTAAAGTATTGAAAAGTAAAATTACATGTTAAGACGTAGTATTAATGGCGAGACTCCTTAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATA                                             <  1:793482/149‑1          AAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGC                                    <  1:1736283/149‑1          AAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGC                                    >  1:1947674/1‑149          AAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGC                                    >  1:304152/1‑149          AAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGC                                    >  1:658782/1‑149           AAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCA                                   >  2:549570/1‑149           AAGTATTTAAAACTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCAGCCTACGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCA                                   >  1:1363285/1‑149            gggggTTAAAAGTAAAATCACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAG                                  <  2:195992/144‑1            AGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGACCAGCAG                                  >  1:777537/1‑149            AGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAG                                  <  2:1842058/149‑1            AGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAG                                  <  1:404641/149‑1            AGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAG                                  >  1:780945/1‑149                ttaAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAAAACAACTTATGGTATAAATAGAGAACAGCAGTAAG                              <  2:1422125/146‑1                tgcAAAAGTAAAATTACATGTTAATACGTAGTATTAATGTCAAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGGACCCTAGGAAAGCTAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAG                              <  2:1821210/146‑1                 gttAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGA                             >  2:1235670/4‑149                 TTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGACATATCGTATAGAAAGAGAACAGCAGTAAGg                             >  1:39527/1‑148                 TTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGA                             >  1:467641/1‑149                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                            >  2:295222/1‑149                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                            >  2:1953747/1‑149                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                            >  2:1653274/1‑149                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                            <  2:1792415/149‑1                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT                            <  1:199610/149‑1                  TAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACGCCTGAAGAAGCAGGACCAGTCGAAGACCGAGGCTGAGACGGCACCCTGAGAAAGCGAAGCCATTCAATACGAAGTGTATTATAAATAGAGAACAGCAGTAAGAT                            >  2:582207/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTCTTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGACACCCTAGGAAAGCGACGCCATTCAATAAGAAGTATTGTATCAAAAGAGAACAACACTTAGATt                           >  2:1374169/1‑148                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAACGCGAAGCCATTCAATACGAAGTATTGTACAAATAGAGAACAGCAGTAAGATA                           >  2:71854/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                           >  2:485270/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                           >  2:233514/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                           >  1:1766749/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                           >  1:404968/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAAAACAGCCGTAAGATA                           >  2:1362515/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATGGTATAAATAGAGAACAGCAGTAAGATA                           >  1:559321/1‑149                   AAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTACTGAGGGAGCAGAGCCAGTAGCAGACCGAGGCTGAGCCGGCACCCTAGGAAAGCGAAGCCATCCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATA                           >  2:472025/1‑149                       GTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGACGTATTGTATCAATAGAGAACAGCAGTAAGATAATTT                       >  2:126991/1‑149                                    TTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCAATTAGAAAATA         <  1:231380/149‑1                                     TAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAATCCATGCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATGATTTTCAATTAGAAAATA         <  2:812928/149‑1                                     TAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATGATTTTCAATTAGAAAATA         <  2:1478548/149‑1                                         ACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTT     <  1:1695626/149‑1                                            TAGTATTAATGGCGAGACTCCTGAGGGATCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATCGTATAAATAGAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACT  <  1:1129155/149‑1                                            TAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGTAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACT  <  2:1161451/149‑1                                                                                                                                                                                                  TATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1205210‑1205323 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATAATTTTTAATTAGAAAATATCTTACT  >  USA300TCH1516_ALE/1205383‑1205460

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