New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	842619 =	194 (0.950)	10 (0.050)	8/144	NT	5.4%	intergenic (+5/‑657)	uvrA/hprK	UvrABC system protein A/HPr kinase/phosphorylase
	?	USA300TCH1516_ALE	842662 =	175 (0.960)					intergenic (+48/‑614)	uvrA/hprK	UvrABC system protein A/HPr kinase/phosphorylase

TAACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/842716‑842619 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttcttttTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAATC  >  USA300TCH1516_ALE/842662‑842751                                                                                                                                                                                              TAACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCAC                                                                                                   <  2:3651910/91‑1  AACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAACTTTATAACATCCTTCACT                                                                                                  >  2:834451/1‑91  AACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACT                                                                                                  <  2:2471302/91‑1   ACATAATTCTTTTTGCGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGATGCGAAGGATAAATTTATAACATCCTTCACTT                                                                                                 <  1:322850/91‑1   ACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTT                                                                                                 >  1:3266658/1‑91   ACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTT                                                                                                 >  1:3269587/1‑91    CATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTC                                                                                                <  2:465155/91‑1      TAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTT                                                                                              <  2:1264908/91‑1      TAATTCGTTTTACGCATCTTTTCTTTCTACTATGCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTT                                                                                              <  2:1264891/91‑1       AATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTT                                                                                             <  1:2248339/91‑1       AATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTT                                                                                             <  1:2248142/91‑1       AATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTT                                                                                             <  2:1285210/91‑1       AATTCTTTTTACGCATCGTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTT                                                                                             <  1:3382648/91‑1        cTTCTTTTTACGCCTCTTTCCTTTCTACTATTCATTACTAGAGTAATAAAAAGAAGCGAAGGATAAATTTATAACACCCTTCACTTCTTTT                                                                                            <  2:3305322/90‑1        ATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTT                                                                                            <  2:2496281/91‑1        ATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTT                                                                                            <  2:2590441/91‑1        ATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTT                                                                                            >  2:3897533/1‑91        ATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACATCTTTT                                                                                            >  2:473870/1‑91         TTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTg                                                                                           >  2:3923271/1‑90                                             CTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGC                                                       >  1:3931082/1‑91                                                     ATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAG                                               >  1:2689661/1‑91                                                      TAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGA                                              >  1:1397736/1‑91                                                        AAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGATAAGATGCGTAAAAAGAAT                                            >  2:457367/1‑91                                                        AAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGATAAGATGCGTAAAAAGAAT                                            >  2:457406/1‑91                                                         AAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATT                                           >  1:3798159/1‑91                                                             AAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGT                                       >  1:581344/1‑91                                                              AGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTT                                      >  2:673574/1‑91                                                              AGCGAAGGATAAATTTATAACATCCTTCACTTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTT                                      >  1:1235019/1‑91                                                                      ATAAATTTATAACATCCTTCGCTTCTTTTTATTAATTTATTAATTAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGG                              >  2:58294/1‑91                                                                                            TTCTTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACA        <  2:2655059/91‑1                                                                                               TTTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAA     >  2:98397/1‑91                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    <  2:1724635/91‑1                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    <  2:952705/91‑1                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    <  2:952168/91‑1                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    <  2:952122/91‑1                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    <  2:952075/91‑1                                                                                                TTTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAA    >  1:2823517/1‑91                                                                                                 TTTATTAATTTAGTAATGCAGAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTACGATCGGGTCTATCTAGAGTAGTTAAACATAAAT   <  2:1380265/91‑1                                                                                                 TTTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAAT   >  2:1802361/1‑91                                                                                                  TTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAATC  >  2:827293/1‑91                                                                                                  TTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAATC  <  1:281198/91‑1                                                                                                  TTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAATC  <  2:1584281/91‑1                                                                                                                                                                                              TAACATAATTCTTTTTACGCATCTTTTCTTTCTACTATTCATTACTAAATTAATAAAAAGAAGCGAAGGATAAATTTATAACATCCTTCACTTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/842716‑842619 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttcttttTATTAATTTAGTAATGAATAGTAGAAAGAAAAGATGCGTAAAAAGAATTATGTTAAGATAGGGTCAATCTAGAGTAGTTAAACATAAATC  >  USA300TCH1516_ALE/842662‑842751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.