New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1758568 =	124 (1.260)	6 (0.070)	4/140	NT	5.6%	intergenic (‑141/+252)	mreC/USA300HOU_RS08780	Cell shape‑determining protein MreC/hypothetical protein
	?	USA300TCH1516_ALE	1758603 =	92 (1.070)					intergenic (‑176/+217)	mreC/USA300HOU_RS08780	Cell shape‑determining protein MreC/hypothetical protein

AGAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1758667‑1758568 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagtagtttAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATAA  >  USA300TCH1516_ALE/1758603‑1758692                                                                                                                                                                                                AGAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGC                                                                                                     >  1:3875838/1‑91 AGAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGATTGC                                                                                                     >  1:3450278/1‑91  GAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCT                                                                                                    <  1:573463/91‑1  GAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCT                                                                                                    >  1:1161711/1‑91  GAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCT                                                                                                    >  1:677750/1‑91    cTTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAG                                                                                                  >  1:1045447/2‑91    ATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAG                                                                                                  >  1:763894/1‑91    ATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAG                                                                                                  >  1:3208735/1‑91    ATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAG                                                                                                  >  1:763920/1‑91    ATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAG                                                                                                  >  1:1045352/1‑91     TTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGT                                                                                                 <  1:655156/91‑1      TCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTA                                                                                                >  1:1340006/1‑91      TCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTA                                                                                                >  1:2418831/1‑91       CGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAG                                                                                               >  1:1148701/1‑91       CGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAG                                                                                               >  1:2619086/1‑91       CGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAG                                                                                               >  1:2381647/1‑91       CGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAG                                                                                               >  1:2605229/1‑91        GAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGT                                                                                              >  1:413783/1‑91        GAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGT                                                                                              <  1:3512533/91‑1         AACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTT                                                                                             <  1:1924575/91‑1         AACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTT                                                                                             <  1:2295435/91‑1         AACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTT                                                                                             <  1:2294444/91‑1         AACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTT                                                                                             >  1:222588/1‑91         AACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTT                                                                                             <  1:1238956/91‑1          ACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTT                                                                                            >  1:3358703/1‑91          ACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTT                                                                                            <  1:3060687/91‑1          ACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTT                                                                                            <  1:3060688/91‑1                                                                TTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACT                                      >  1:1596354/1‑91                                                                 TAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTG                                     >  1:1065515/1‑91                                                                 TAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTG                                     >  1:3419130/1‑91                                                                  AAACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGT                                    >  1:1383580/1‑91                                                                   AACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTT                                   >  1:3077181/1‑91                                                                   AACTACTAGTGACTGGAATGTTTGCTAGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTT                                   >  1:3077989/1‑91                                                                                             AGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTG         >  1:1801862/1‑91                                                                                             AGTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTG         >  1:3339965/1‑91                                                                                              GTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGC        >  1:3248455/1‑91                                                                                              GTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGC        >  1:709104/1‑91                                                                                              GTAGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGC        <  1:2903103/91‑1                                                                                                AGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGA      <  1:1088105/91‑1                                                                                                AGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGA      >  1:3691735/1‑91                                                                                                AGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGA      <  1:3715407/91‑1                                                                                                AGTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGA      >  1:827616/1‑91                                                                                                 GTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAA     <  1:2512993/91‑1                                                                                                 GTTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAA     <  1:2514176/91‑1                                                                                                  TTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAAT    <  1:869748/91‑1                                                                                                  TTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAAT    <  1:3044278/91‑1                                                                                                  TTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAAT    <  1:2521639/91‑1                                                                                                  TTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAAT    <  1:2521020/91‑1                                                                                                  TTTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAAT    <  1:2218926/91‑1                                                                                                   TTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATA   <  1:3018215/91‑1                                                                                                   TTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATA   >  1:2955650/1‑91                                                                                                   TTAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATA   <  1:2575746/91‑1                                                                                                    TAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATAA  >  1:3269135/1‑91                                                                                                                                                                                                AGAATTCGAACAGTGAATCCTCGAACGATACAAACAAATAATTTTAAAATTTAAATCGATTATTTAAACTACTAGTGACTGGAATGTTTGCTAGTAGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1758667‑1758568 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagtagtttAAATAATCGATTTAAATTTTAAAATTATTTGTTTGTATCGTTCGAGGATTCACTGTTCGAATTCTGAAGTTGTCTCCAACGTGCGAATAA  >  USA300TCH1516_ALE/1758603‑1758692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.