New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_012417	1 =	0 (0.000)	31 (0.020) +ATAAAAAGAC	8/140	NT	5.5%	intergenic (–/‑279)	–/USA300HOU_RS14890	–/replication protein
	?	NC_012417	3071 =	1228 (0.590)					intergenic (‑397/–)	USA300HOU_RS14900/–	hypothetical protein/–

TTTTATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_012417/49‑1 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT‑‑‑‑  >  NC_012417/3071‑3125                                                  ||||||||||                                                            TTTTATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAG‑‑‑TATTATTAAGGTGTCGAATCTTAAAT                          <  1:521648/91‑1 TTTTATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAG‑‑‑TATTATTAAGGTGTCGAATCTTAAAT                          <  1:1941402/91‑1   TTATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAG‑‑‑TATTATTAAGGTGTCGAATCTTAAATAA                        <  1:3317566/91‑1    TATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAG‑‑‑TATTATTAAGGTGTCGAATCTTAAATAAT                       <  1:1690489/91‑1     ATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATA                         <  1:3277709/91‑1     ATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATAT‑AAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAA                        <  1:1287331/91‑1      TTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCTAATCTTAAATAA                        <  1:1206271/91‑1       TATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAAT                       <  1:393753/91‑1       TATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAAT                       <  1:754574/91‑1       TATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAAT                       <  1:2677353/91‑1       TATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAAT                       <  2:882919/91‑1       TATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAAT                       <  1:2136963/91‑1        ATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATA                      <  2:3811164/91‑1           TTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGG                 <  1:2665932/91‑1             GATTTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGG                 <  1:1167452/91‑1                TTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGT              <  2:1382288/91‑1                TTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGACCCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGT              <  1:2280580/91‑1                TTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAAGA‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTC             <  1:1244843/91‑1                TTTCGGTTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCT            <  1:3410260/91‑1                   CGGTTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTT         <  1:2687473/91‑1                    GGTTATACTTCTAGTAGTATTATATTGCATATAAAAA‑AACCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTT         <  2:906127/91‑1                    GGTTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTT        <  1:3007771/91‑1                      TTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  1:3733495/91‑1                      TTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  1:3732954/91‑1                      TTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  1:358781/91‑1                      TTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  2:3489195/91‑1                      TTATACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  1:2447209/91‑1                       TATACTTCTAGTAGTATTATATTGCATATAAAAA‑AACCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT      <  1:2827542/91‑1                         TACTTCTAGTAGTATTATATTGCATATAAAAA‑AACCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTATat    <  1:2632504/91‑3                          ACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTATatgc  <  2:454248/91‑5                          ACTTCTAGTAGTATTATATTGCATATAAAAA‑A‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTATatgc  <  1:2069639/91‑5                                                  ||||||||||                                                            TTTTATTATCTTGATTTTCGGTTATACTTCTAGTAGTATTATATTGCAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_012417/49‑1 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CCCCAGTTATATTATTAAGGTGTCGAATCTTAAATAATACTGGGGGTCTTTTTAT‑‑‑‑  >  NC_012417/3071‑3125

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.