New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2001491 =	11 (0.170)	3 (0.050)	3/244	NT	22.4%	intergenic (‑100/+116)	rrl3/USA300HOU_t0051	23S ribosomal RNA/tRNA‑Ala
	?	CP000730	2179606 =	NA (NA)					intergenic (‑50/+262)	rrl4/rrs4	23S ribosomal RNA/16S ribosomal RNA

CTAGTGCCAAGGCATCCACCGTGCGCCCTTAATAACTTAATCTATGTTTCCACCATTTTTATAAGTCAAACGTTAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGAT  >  CP000730/2001352‑2001625                                                                                                                                            |                                                                                                                                       gcgagcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagttaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaag                                                                                                                                        >  2:573992‑M1/140‑140 (MQ=255)  cgagcgcttgactaaaaagaaattgtacattgaaaactagataattaagtaaattccccagtcgaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGa                                                                                                                                       >  1:166532‑M1/139‑140 (MQ=255)  cgagcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGa                                                                                                                                       <  2:573458‑M1/2‑1 (MQ=255)  cgagcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGa                                                                                                                                       >  2:109607‑M1/139‑140 (MQ=255)  agagagcttaactaaaaagaaattgtacatggaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgaattactaaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGa                                                                                                                                       >  1:351255‑M1/139‑140 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAaca                                                                                                                                    <  1:250259‑M1/5‑1 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAaca                                                                                                                                    <  1:50184‑M1/5‑1 (MQ=255)     gcgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgatcgaaaGAaca                                                                                                                                    <  2:297186‑M1/5‑1 (MQ=255)      cgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                   >  1:395715‑M1/135‑140 (MQ=255)      cgcttgactaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                   >  1:565406‑M1/135‑140 (MQ=255)      cgctagactaaaaagaaatagtacatttataactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaattaagcttgaattcataagaaataatcgctagtgttcgaaaGAacac                                                                                                                                   >  2:463333‑M1/135‑140 (MQ=255)            actaaaaagaaattgtacattgaaaactagataagtaagtaaactatagcttttaccaagcaaagccgagtcaataaagaggtttaaataagattgaattgataagaaaaaatggctattgtgcgaaaGAAcactaacaa                                                                                                                             <  2:605817‑M1/12‑5 (MQ=255)            actaaaaagaaattgtacattgaaaactagataagtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaaataagcttgaaatcataagaaataatcgctagtgttcgaaagaacacacccaa                                                                                                                             <  1:81814‑M1/12‑7 (MQ=255)             tatgcACCGTGCGTCCTTAATAACTTAATCTATGTTTCCACCATTTTTATAAGTCAAACGTTAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGat                                                                                                                            <  1:300462/136‑1 (MQ=0)                                       aaccTATGTTTCCATCATTTTTATATTTCAAACCTTAACTTGAAGTTACTTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTCTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTAttt                                                                                                  <  1:264382/137‑1 (MQ=1)                                              gtaagtaaaatatagattttaccaagcaaaaccgagtgaataaagagttttaataactctataattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAActc                                                                                           >  1:712630‑M1/95‑140 (MQ=255)                                                     aaatatagattttaacaagcaaaatcgagttaataaagagttttaaataagcttgtattcataagaaataatcgctagtgttctttcGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTc                                                                                    >  1:15305‑M1/88‑140 (MQ=255)                                                                                                                 cggtattaATCTTGTGAGTGTTCTTTCGAACACTAGCGA‑TATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAaat                       <  2:638670/137‑1 (MQ=0)                                                                                                                           cTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGga              <  2:449613/140‑1 (MQ=11)                                                                                                                           atcgctagtgttcgaaaGAACACTAGCGATTATTACTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTACAATCTATATTTTAGTTACTTATCAAGTTTTCAATGTACAAATAATGGTGga              <  2:435506‑M1/123‑1 (MQ=255)                                                                                                                               tgAGTGTTCTTTCGTTCACTAGCGATTATTTCTTATGTATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCATTGTACAAATAATGGTGGAGACt          <  1:224750/140‑1 (MQ=255)                                                                                                                               tgAGTGTTCTTTCCAACATTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACt          <  2:112267/140‑1 (MQ=18)                                                                                                                                gAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTa         <  2:188742/140‑1 (MQ=34)                                                                                                                                 aGTGTTCTTTCGAAAACTAGCGAATATTTCTTATGAATTAAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTATTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAAACTAg        >  2:351532/1‑140 (MQ=11)                                                                                                                                   tgtTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCg      >  2:466902/1‑140 (MQ=37)                                                                                                                                     ttCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTATGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAACTAATGGTGGAGACTAGCggg    >  2:19814/1‑140 (MQ=255)                                                                                                                                     atCTTTCGTACACTAGCGTTTATTTCTTATGAATTCAAGCTTATTTTAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCggg    <  1:369201/139‑1 (MQ=255)                                                                                                                                       cTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCTGGAt  >  2:528599/1‑140 (MQ=38)                                                                                                                                            |                                                                                                                                       CTAGTGCCAAGGCATCCACCGTGCGCCCTTAATAACTTAATCTATGTTTCCACCATTTTTATAAGTCAAACGTTAACATGAAGTTACGTTCTTTTATAAAAAGATTTAAACGCGTTATTAATCTTGTGAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGAGACTAGCGGGAT  >  CP000730/2001352‑2001625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.