New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1759680	90 (0.920)	8 (0.100)	7/132	NT	10.5%	intergenic (‑387/+87)	USA300HOU_RS08780/USA300HOU_RS08785	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1759708	62 (0.760)					intergenic (‑415/+59)	USA300HOU_RS08780/USA300HOU_RS08785	hypothetical protein/hypothetical protein

AAGGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1759577‑1759680 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaactcctaatgtGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTAAA  <  USA300TCH1516_ALE/1759708‑1759623                                                                                                                                                                                                AAGGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACA                                                                                                     <  1:458399/91‑1  AGGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAA                                                                                                    <  1:1885470/91‑1   GGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAA                                                                                                   <  1:733614/91‑1   GGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAA                                                                                                   <  1:618811/91‑1    GTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAA                                                                                                  >  1:2304700/1‑91    GTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAA                                                                                                  >  1:2304205/1‑91     TTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAAC                                                                                                 <  1:2830190/91‑1      TTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACT                                                                                                >  1:768563/1‑91      TTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACT                                                                                                >  1:2180965/1‑91        AATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCC                                                                                              >  1:721768/1‑91         ATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCT                                                                                             <  1:4003124/91‑1          TTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTA                                                                                            >  1:1833545/1‑91           TTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAA                                                                                           >  1:1549659/1‑91            TGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAAT                                                                                          >  1:469513/1‑91             GGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATG                                                                                         <  1:1957181/91‑1             GGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATG                                                                                         <  1:2317782/91‑1              GTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT                                                                                        >  1:1349788/1‑91              GTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT                                                                                        <  1:2025520/91‑1              GTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT                                                                                        >  1:2159326/1‑91              GTTGCTCGATTATTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT                                                                                        <  1:3756899/91‑1                                    AATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAA                                                                  >  1:3659582/1‑91                                     ATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT‑‑‑ACTAGTTAAAAAATTCTAAACTA                                                              <  1:2989455/91‑1                                      TAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT‑‑‑ACTAGTTAAAAAATTCTAAACTAG                                                             <  1:1944909/91‑1                                          GGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGT                                                            <  1:2702621/91‑1                                          GGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGT                                                            <  1:2702679/91‑1                                             TTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACA                                                         <  1:35578/91‑1                                              TTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACAT                                                        <  1:3077771/91‑1                                                   CCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGA                                                   <  1:1179500/91‑1                                                                                           AAAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAG           >  1:228056/1‑91                                                                                            AAACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGT          <  1:3776155/91‑1                                                                                              ACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGC        <  1:1525577/91‑1                                                                                              ACTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGC        <  1:1723304/91‑1                                                                                               CTCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCG       <  1:571031/91‑1                                                                                                TCCTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGG      <  1:2247411/91‑1                                                                                                  CTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTA    <  1:533624/91‑1                                                                                                  CTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTA    <  1:534016/91‑1                                                                                                  CTAATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTA    <  1:534230/91‑1                                                                                                    AATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTAAA  <  1:3920114/91‑1                                                                                                    AATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTAAA  >  1:1837471/1‑91                                                                                                    AATGTGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTAAA  >  1:2413438/1‑91                                                                                                                                                                                                AAGGTTTAATTTGGTTGCTCGATTTTTTTCAAATAAATAGTGGATTTTTACCGCACTTTCAATTTAACAATTAAATTTATTCTGCATAACAAAACTCCTAATGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1759577‑1759680 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaactcctaatgtGGAACTAGTTAAAAAATTCTAAACTAGTACATTAGGAGTTTTGTTATGCAGAATAAATTTAATTGTTAAATTGAAAGTGCGGTAAA  <  USA300TCH1516_ALE/1759708‑1759623

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