New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1682523	194 (0.950)	24 (0.130)	13/140	NT	12.6%	intergenic (‑268/+36)	USA300HOU_RS08380/USA300HOU_RS08385	PhoH‑like protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1682539	164 (0.920)					intergenic (‑284/+20)	USA300HOU_RS08380/USA300HOU_RS08385	PhoH‑like protein/hypothetical protein

AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1682424‑1682523 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaacaagcaCTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  USA300TCH1516_ALE/1682539‑1682450                                                                                                                                                                                                AATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAA                                                                                                     >  2:3466787/1‑91  ATTTTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAA                                                                                                    <  2:1865157/91‑1     TTAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAAC                                                                                                 <  2:449575/91‑1      TAGACTAATCAATTTTTTGCTGTAATTTAAATAACTAAAAAAAAAAAAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACA                                                                                                <  2:1804927/91‑1       AGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAA                                                                                               >  2:3884237/1‑91       AGACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAA                                                                                               <  1:1810969/91‑1        GACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAG                                                                                              >  2:662156/1‑91         ACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGC                                                                                             <  2:1378181/91‑1         ACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGC                                                                                             <  2:1378139/91‑1         ACTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGC                                                                                             <  2:1378122/91‑1          CTAATCAATTTTTTGTTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAACAAACAAGCA                                                                                            >  2:585369/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  2:2676464/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  1:3734504/1‑91          CTAATCAATTTTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCA                                                                                            >  1:3734622/1‑91           TAATCAATTCTTTGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTATTTTTTATTAACGTAAAATAACCAGtaa                                                                                           >  2:514025/1‑88                       TGCTGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGT                                                                               <  2:42084/91‑1                          TGTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGT                                                                            <  2:3722651/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  2:462354/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  2:3167542/91‑1                           GTAATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTATAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTT                                                                           <  1:3147583/91‑1                            TAATTTAAATAACTAATATTTCTCGAAAAATTATCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTG                                                                          <  1:3380545/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  2:1806052/91‑1                             AATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGC                                                                         <  1:985807/91‑1                              ATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  1:2187109/91‑1                              ATTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCT                                                                        <  1:2187110/91‑1                               TTTAACTAACTAGTATTTCTCGAAAAATTCTCTTTGTTTTGTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTT                                                                       <  2:3636808/91‑1                               TTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTATCGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTT                                                                       <  2:3865436/91‑1                               TTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTT                                                                       <  1:158843/91‑1                               TTTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTT                                                                       <  2:51301/91‑1                                TTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTG                                                                      <  1:911951/91‑1                                TTAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTAGCGTAATGGTAGTTGCTTG                                                                      <  2:1823004/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  1:3538267/91‑1                                 TAAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGT                                                                     <  1:2591305/91‑1                                  AAATAACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTT                                                                    <  2:1617838/91‑1                                       ACTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTT                                                               <  1:2473557/91‑1                                        CTAATATTTCTCGAAAAATTCTCTTTGTTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTA                                                              <  1:2785491/91‑1                                                                   TTTTTTAATTTTTCTTAGCATAAAAAAACAAGCACTATCGTAATGGTAGTTTCTTGTTTTTTTGCGTTAAGAAAAATTAAAAAACAAAGAG                                   <  1:1508765/91‑1                                                                   TTTTTTAATTTTTCTTAACGTAAAAAAACAAGCTATATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAG                                   <  1:1508766/91‑1                                                                   TTTTTTAATTTTTCTTAACGTAAAAAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAG                                   <  1:1508775/91‑1                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGTAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  2:3045858/91‑1                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGGAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  2:3046290/91‑1                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  2:2192293/91‑1                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  2:2839868/91‑1                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           >  1:1624042/1‑91                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           >  1:54668/1‑91                                                                                           AAAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAAAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTAT           <  2:2840294/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  2:3737182/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  2:765492/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  1:1319567/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  2:633367/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  1:3081218/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  2:3775302/91‑1                                                                                            AAACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATT          <  2:1271927/91‑1                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         <  1:3642147/91‑1                                                                                             AACAAGCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTT         <  1:2063149/91‑1                                                                                                  GCACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATT    >  2:595865/1‑91                                                                                                  GCACTAACGCAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATCACAAAACAAAGAGAATTTTTCGAGAAATAATAGTTAGTTAAATT    >  2:251122/1‑91                                                                                                   CACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTA   <  1:836583/91‑1                                                                                                   CACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTA   >  2:1595933/1‑91                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  >  2:1757173/1‑91                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  2:1226793/91‑1                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  2:1598888/91‑1                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTTTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  >  2:1901931/1‑91                                                                                                    ACTATCGTAATGGTAGTTGCTTGTTCTTTTACGTTAAGAAAAATTAAAAAACAAAGAGAATTTTTCGAGAAATATTAGTTATTTAAATTAC  <  1:3688805/91‑1                                                                                                                                                                                                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 < 12 ≤ ATCG/ATCG < 32 ≤ 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.