New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1682523	145 (0.760)	34 (0.200)	16/140	NT	21.5%	intergenic (‑268/+36)	USA300HOU_RS08380/USA300HOU_RS08385	PhoH‑like protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1682539	122 (0.730)					intergenic (‑284/+20)	USA300HOU_RS08380/USA300HOU_RS08385	PhoH‑like protein/hypothetical protein

AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1682424‑1682523 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaacaagcaCTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  USA300TCH1516_ALE/1682539‑1682450                                                                                                                                                                                                AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAA                                                                                                     <  1:1725940/91‑1 AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAA                                                                                                     >  1:2791272/1‑91  ATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATATCTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAA                                                                                                    >  1:3285277/1‑91  ATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAA                                                                                                    >  2:2243484/1‑91  ATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAA                                                                                                    >  1:403067/1‑91   TTTTAGACTCATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACATAAAAAA                                                                                                   >  1:1947153/1‑91   TTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAA                                                                                                   >  2:85010/1‑91    TTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAA                                                                                                  <  1:1328729/91‑1    TTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAA                                                                                                  <  1:1328850/91‑1     TTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAAC                                                                                                 >  2:256764/1‑91      TAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACA                                                                                                >  2:2853688/1‑91       AGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAA                                                                                               >  1:393217/1‑91       AGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAA                                                                                               <  2:2329517/91‑1        GACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAG                                                                                              <  2:338587/91‑1         ACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGC                                                                                             <  1:958061/91‑1         ACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGC                                                                                             <  1:393067/91‑1          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  2:683611/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  2:1777327/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  2:683447/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGCTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  2:685487/1‑91                  TTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTA                                                                                    <  1:3439542/91‑1                  TTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTA                                                                                    <  1:2785226/91‑1                  TTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTA                                                                                    <  1:928243/91‑1                    TTTTGCTGTAATTTAAATAACTAACATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAAT                                                                                  <  2:3619247/91‑1                      TTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGG                                                                                <  1:379841/91‑1                          TGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGT                                                                            <  1:1543214/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  2:2566102/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  1:2435157/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  1:2434996/91‑1                            TAATTTAAATAACTAATATTTCTCGTAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTG                                                                          <  1:3627570/91‑1                            TAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAA‑TTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  2:2231371/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAGTGGTAGTTGC                                                                         <  2:2419763/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  2:1688940/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  2:1440437/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  1:964916/91‑1                              ATTTAAATAACTAATATTTCTCGACAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  2:3605107/91‑1                              ATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  2:300646/91‑1                              ATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  2:300525/91‑1                              ATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  2:300496/91‑1                               TTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTT                                                                       <  2:1506047/91‑1                                TTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTG                                                                      <  1:2669763/91‑1                                TTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTG                                                                      <  1:732557/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  2:3587306/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  2:491086/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  2:653982/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  1:3215624/91‑1                                  AAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTT                                                                    <  1:3539670/91‑1                                   AATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTT                                                                   <  2:411303/91‑1                                        CTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTA                                                              <  1:3423260/91‑1                                        CTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTA                                                              <  1:1793519/91‑1                                            TATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTT                                                          <  1:1339962/91‑1                                                                    TTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGA                                  <  1:438733/91‑1                                                                    TTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGA                                  <  1:438749/91‑1                                                                    TTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGA                                  <  1:439365/91‑1                                                                                           AAAACGAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           >  2:3554011/1‑91                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           >  2:486288/1‑91                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  1:1291129/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  1:2244799/91‑1                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         <  1:645855/91‑1                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         >  1:635355/1‑91                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         <  1:3246765/91‑1                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         >  1:1802320/1‑91                                                                                                 AGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAAT     >  2:569052/1‑91                                                                                                  GCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATT    >  2:1689577/1‑91                                                                                                  GCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATT    >  2:3683360/1‑91                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  1:469367/91‑1                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  >  1:2489424/1‑91                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  >  1:2217739/1‑91                                                                                                                                                                                                AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1682424‑1682523 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaacaagcaCTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  USA300TCH1516_ALE/1682539‑1682450

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.