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Read depths from cell cultured viral samples were higher, with average read depths of 31 (RV20 depleted), 125 (RV20) and 65 (RV2324 cell pellet) and maximum read depths of 69 (RV20 depleted), 228 (RV20) and 272 (RV2324 cell pellet).
We find that transcriptional programs can be reproducibly identified at 1% of conventional read depths.
CCF values were normalized by respective read depths and used as variant frequencies for input into PhyloWGS.
For all eight patients, 81-84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322× to 798×.
Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples.
Regions of read depths <15 were first filtered out.
Validation dataset RRBS and RNA-seq read depths.
Adult female Duroc RRBS and RNA-seq read depths.
Regions with read depths of < 10× were not analyzed further.
Diminishing returns are only seen at much higher read depths.
To assess performance at low read depths (≤15×), 10 S.
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