New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1046337	153 (0.750)	10 (0.050)	6/148	NT	6.6%	coding (477/939 nt)	menA	1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
	?	USA300TCH1516_ALE	= 1046354	143 (0.760)					coding (460/939 nt)	menA	1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase

ACTATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1046242‑1046337 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcctTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATGT  <  USA300TCH1516_ALE/1046354‑1046266                                                                                                                                                                                           ACTATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATA                                                                                                >  2:779091/1‑91  CTATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATAC                                                                                               <  2:1318350/91‑1    ATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGTATAAAGAATGCAATAACGATAATAAACATAACCATAAATAAGC                                                                                             >  2:13212/1‑91    ATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGg                                                                                             >  2:3917206/1‑90    ATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGC                                                                                             >  2:549600/1‑91     TAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCC                                                                                            >  2:2224009/1‑91     TAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCC                                                                                            <  2:2962244/91‑1      AGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCT                                                                                           <  2:959072/91‑1      AGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCT                                                                                           >  2:813758/1‑91      AGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGATTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCT                                                                                           <  2:3471714/91‑1                  CCAGATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGAGAATTA                                                                               <  1:3069271/91‑1                  CCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTA                                                                               <  1:2661976/91‑1                         ACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAG                                                                        <  2:3135520/91‑1                         ACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAG                                                                        <  2:3135397/91‑1                          CATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGG                                                                       <  2:2427494/91‑1                          CATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGG                                                                       <  2:2426980/91‑1                           ATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGGC                                                                      <  1:1040217/91‑1                            gAACTTTGGATATTGCCAGTTTGAATAGAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGGCG                                                                     <  2:1776215/90‑1                            TAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGGCG                                                                     >  2:1790318/1‑91                            TAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTTTCGGTGAATTATTCTCAGGCG                                                                     <  2:2797136/91‑1                                                                                          ggCGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGT       <  2:1035816/89‑1                                                                                           ACGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTT      <  2:1923009/91‑1                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     <  1:130540/91‑1                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     <  1:2015013/91‑1                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     >  2:3250276/1‑91                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     >  2:2815002/1‑91                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     >  1:2880643/1‑91                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTA     <  1:787852/91‑1                                                                                            CGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTAAAAGTTA     >  2:3511780/1‑91                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    <  1:3774643/91‑1                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    <  1:2772198/91‑1                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    >  1:2715554/1‑91                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    <  1:2669368/91‑1                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    <  1:2668103/91‑1                                                                                             GCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTAT    <  1:2626784/91‑1                                                                                              CCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATG   >  1:3836836/1‑91                                                                                              CCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATG   <  2:3808554/91‑1                                                                                              CCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATG   >  1:1533033/1‑91                                                                                              CCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATG   >  2:1112125/1‑91                                                                                               CTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATGT  >  2:2717644/1‑91                                                                                               CTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATGT  >  1:2192271/1‑91                                                                                                                                                                                           ACTATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1046242‑1046337 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcctTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATGT  <  USA300TCH1516_ALE/1046354‑1046266

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.