| New junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 514610 | NA (NA) | 6 (0.050) | 6/244 | NT | 23.2% | intergenic (+2678/‑4085) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 558903 | 21 (0.170) | intergenic (+116/+3686) | USA300TCH1516_00505/gabR | tRNA‑Ile/HTH‑type transcriptional regulatory protein GabR | |||||
GGTTCGAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGT > USA300TCH1516_ALE/558763‑559043 | ggtTCGAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTC < 2:584246‑M2/141‑1 (MQ=255) tCGAGTCCACTTAGGTCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGaa < 1:900365/141‑1 (MQ=255) tCGAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGaa > 4:270513/1‑141 (MQ=255) gAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCtttcg > 3:356067‑M2/1‑136 (MQ=255) gAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAg < 1:12556/141‑1 (MQ=40) gAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAg < 4:51551/141‑1 (MQ=40) aGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGa < 1:845391/141‑1 (MQ=40) gTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCtttcgaa > 1:658526‑M2/1‑134 (MQ=255) gTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGaa < 1:325993/141‑1 (MQ=39) gTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGATTTACATTAGCTGGAGTATATAAGAAATAATTGCTAGTGTTCGAAAGaa > 1:754134/1‑141 (MQ=14) ccACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAaca < 1:242873/141‑1 (MQ=38) cACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAacac > 2:840094/1‑141 (MQ=37) aCTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACt > 4:262889/1‑141 (MQ=35) aCTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACt > 1:998413/1‑141 (MQ=35) cTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTc > 1:795190/1‑141 (MQ=35) taagCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGGGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTcac < 2:609203/138‑1 (MQ=14) tAGGCCCACCATTATTTNNACATTGAAAACTAGNTAANTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTAGAAAGAAAACTcac > 1:903426/1‑141 (MQ=255) tAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTcac > 2:1029740/1‑141 (MQ=33) aGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCtttcgaacactagcg > 3:20670‑M2/1‑126 (MQ=255) aGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTcaca > 1:175451/1‑141 (MQ=32) ggCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACaa < 1:405377/141‑1 (MQ=32) ggCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTAGAAAGACCACTCACaa > 1:48024/1‑141 (MQ=17) gCCCANCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAg < 3:125647/141‑1 (MQ=14) gCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGCGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAg > 1:212619/1‑141 (MQ=14) gCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAATAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAg < 2:703846/141‑1 (MQ=14) accttGAAAACTAGATAAGTAAGTAAAATATAGAATTTACAAAGCAAAACCGAGTGAATAAAGAGATTTAAATAAGCCTGAAATCATAAGAAATAATCGCTAGTGTCCGAAAGAACAACAACAAGATTAATAACGCGTTTc > 2:539936/4‑141 (MQ=1) aagataGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGt < 1:22158/138‑1 (MQ=1) ccaaGTGAAAAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTTTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGTATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGc < 2:265021/138‑1 (MQ=0) aaTAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCgaaagaacactagcgattatttcttatgaattcaagcttatttaaaactctttatt < 3:250111‑M2/108‑57 (MQ=255) aaTAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCgaaagaacactagcgattatttcttatgaattcaagcttatttaaaactctttatt > 4:250111‑M2/1‑52 (MQ=255) agTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCgaaagaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttactt < 1:286816‑M2/141‑97 (MQ=255) tAAGAAATAGTCGCTAGTGTTCgaaagaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaaata < 1:952710‑M2/141‑120 (MQ=255) aagaatCGCTATTTTTCTAAAGAACGCTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGTATGCCGTGGCACGAGAAGGCGATGATGGACGTGACGTACCACGata < 4:65129/138‑1 (MQ=1) tCGCTAGTGTTCgaaagaacactagcgattatttcttatgaattcaagcttatttaaaacgctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtc < 1:294231‑M2/141‑130 (MQ=255) aGTGTTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaagctctttattcactcggttttgcttggtaaaatctctattttacttacttatctagttttcaatgtgcagtttctttttcgtcaaacg > 2:428175‑M2/1‑7 (MQ=255) aGTGTTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcg < 1:60783‑M2/141‑135 (MQ=255) aGTGTTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcg < 3:248409‑M2/141‑135 (MQ=255) aGTGTTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcg < 3:217355‑M2/141‑135 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 2:531845‑M2/141‑136 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 3:416392‑M2/141‑136 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 2:1060769‑M2/141‑136 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 2:829925‑M2/141‑136 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 2:37505‑M2/141‑136 (MQ=255) gtgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc > 2:277084‑M2/1‑6 (MQ=255) gtgtTCtttcgaacactagcgattatctcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgc < 1:399842‑M2/141‑136 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 4:352234‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 1:448098‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct > 1:1015010‑M2/1‑5 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 1:757388‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 2:567146‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct > 4:378939‑M2/1‑5 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 2:908804‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct < 1:203838‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgct > 2:796991‑M2/1‑5 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagtttgcaatgtacaatttctttttagtcaagcgct < 4:301200‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaaactatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgcg < 2:186098‑M2/141‑137 (MQ=255) tgtTCtttcgaacactagcgattatttcttatgaattactaccagggtaaaactcttgattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttattcaagcgct < 1:792481‑M2/141‑137 (MQ=255) gtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctc > 1:997763‑M2/1‑4 (MQ=255) gtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctc < 3:304291‑M2/141‑138 (MQ=255) gtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctc < 1:465863‑M2/141‑138 (MQ=255) gtTCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactatttcttaacaaggtcttgcttggtaaaatctatattttacttacttatcgagttttcaatgtacaatttctttttagtcaagcgctc > 3:201039‑M2/1‑4 (MQ=255) ttCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttctatgtacaatttctttttagtcaagcgctcg < 4:46726‑M2/141‑139 (MQ=255) ttCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcg > 3:331048‑M2/1‑3 (MQ=255) ttCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcg > 3:242281‑M2/1‑3 (MQ=255) ttCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcg < 2:699284‑M2/141‑139 (MQ=255) ttCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagccctct < 4:89490‑M2/141‑139 (MQ=255) ttCtctcgaacactagcgatcatgtcttatgaattccagcttatttaaaactcgttcttcactcggttttgcttggtaaaatctatattttacttacttatctagtttccaatgtacaatttctatttagtcaagcgctcg < 4:404232‑M2/141‑139 (MQ=255) tCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcgc < 3:425888‑M2/141‑140 (MQ=255) tCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcgc < 2:35798‑M2/141‑140 (MQ=255) tCtttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcgc < 2:317155‑M2/141‑140 (MQ=255) ctttcgaacactagcgattatttcttatgaattcaagcttatttaaaactctttattcactcggttttgcttggtaaaatctatattttacttacttatctagttttcaatgtacaatttctttttagtcaagcgctcgca > 3:112793‑M2/1‑1 (MQ=255) | GGTTCGAGTCCACTTAGGCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGT > USA300TCH1516_ALE/558763‑559043 |
| 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. |