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Under the conditions tested, exome data did not provide such high levels of detection and prediction accuracy at any read depth and performance for predicting individual protein coding alleles from exome data was uniformly poor.
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Interspersed within this sequence were 51 regions not covered by any reads or covered at a read depth of 1× only.
We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of ≥3, 86% at a read depth of ≥10, and over 50% of all targets were covered with ≥20 reads.
Two of these (nucleotide positions 2,614 and 10,045) were covered at a read depth of only 2× and exhibited ambiguous nucleotides.
The maximum coverage was obtained at position 4832 of the reference genome in the p31 int region of the pol gene at a read depth of 951,240 (Figure 3A).
For these sequence-poor regions, no sequence information was obtained for 420 nucleotide positions of the reference sequence and 581 nucleotide positions were covered at a read depth of 1×.
Simple SNPs were consistently represented at lower levels still (62.37% at a read depth of 10).
At a read depth of 2X, 13,964 genes were expressed in at least one tissue/treatment combination (data not shown).
At a read depth of 3X or higher, the Agilent V2 captured 92% of the CCDS cardiac gene region.
However, to compare overall capture between various capture kits, regions covered at a read depth of at least 3X were included.
Regardless of differences in read length, genomic coverage was very high with more than 99.5% of the reference genome covered at a read depth of 10 or greater.
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