New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2693368 =	85 (0.860)	6 (0.070)	5/234	NT	7.6%	intergenic (+39/+38)	USA300HOU_2547/USA300HOU_2548	TetR family transcriptional regulator/hypothetical protein
	?	CP000730	2693417 =	69 (0.770)					coding (157/168 nt)	USA300HOU_2548	hypothetical protein

ACAACTGAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2693517‑2693368 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actatcgtttttTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTATT  >  CP000730/2693417‑2693556                                                                                                                                                                                                                                                                                                       ACAACTGAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTTTTTTTATTTTATGTGTAGTGTGTAAGTTGTTTTATTAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑AGTGTAC‑Aaa                                                                                                                                                       >  2:551552/1‑139    ACTGAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATC                                                                                                                                                    >  1:1180424/1‑141    ACTGAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATC                                                                                                                                                    <  1:827915/141‑1       GAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTT                                                                                                                                                 >  1:911998/1‑141       GAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTT                                                                                                                                                 >  1:495330/1‑141        AGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTCATGTGAATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGACTTCATTAA‑‑CGTGTAC‑ACcctggcca                                                                                                                                                >  2:838332/1‑133        AGTCAAAGACATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGCATTCATTAA‑‑CGTGTAC‑ACTATCGTTT                                                                                                                                                >  2:751176/1‑141                                             TCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGTTAAGCACGATAAAAATAAAAAACGATAGT‑GTACACG‑‑TTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTG                                                                                                           <  1:398238/141‑1                                                                                                         AACGATAGTAGTACACGAATTCATTAA‑‑CGCGTAC‑ACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTC                                               >  2:664778/1‑141                                                                                                                GTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTT                                        >  2:627446/1‑141                                                                                                                GTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTT                                        >  2:150595/1‑141                                                                                                                   GTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAA                                     >  2:1163091/1‑141                                                                                                                       ACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGA                                 <  1:627446/141‑1                                                                                                                                                TATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCC           >  2:319143/1‑141                                                                                                                                                 ATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGTTATCTAAATGACTTTGACTCATTTGTTTAAATGACCAAATGGCTAATACAATTCCCA          <  2:708480/141‑1                                                                                                                                                 ATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCA          >  1:1059385/1‑141                                                                                                                                                   CGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATT        >  1:539767/1‑141                                                                                                                                                   CGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCACATT        >  2:1058709/1‑141                                                                                                                                                     TTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTAT      >  2:336676/1‑141                                                                                                                                                        TTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTAT   <  2:292098/141‑1                                                                                                                                                        TTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTAT   <  2:687936/141‑1                                                                                                                                                        TTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTAT   <  1:843174/141‑1                                                                                                                                                        TTTATTTTTATCATGCTTATCGCTATTCAAACAACTAATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTAT   <  1:531887/141‑1                                                                                                                                                         TTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTATT  >  1:686796/1‑141                                                                                                                                                         TTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTATT  >  2:732704/1‑141                                                                                                                                                         TTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTATT  >  1:508782/1‑141                                                                                                                                                                                                                                                                                                       ACAACTGAGTCAAAGTCATTTAGATAGCGGATTTATTTTTTTCTTCATAGTTTATGTGTTGTGTATCAGTTGTTTTAATAGCGATAAGCACGATAAAAATAAAAAACGATAGTAGTACACGAATTCATTAA‑‑CGTGTAC‑ACTATCGTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2693517‑2693368 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actatcgtttttTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGACTTTGACTCAGTTGTTTAAATGACCAAATTGCTAATACAATTCCCATTATTATT  >  CP000730/2693417‑2693556

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