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All samples were sequenced to a minimum average coverage of 36× (Table 1).
The BAC clones were sequenced to a minimum six-fold coverage using Sanger sequencing methods on ABI 3730 xl by the company GATC, Germany.
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These BAC clones are being sequenced to a minimum of 4-fold sequence coverage.
Whole genomes will be sequenced to a minimum depth of 30× reads average coverage depth while exomes will be sequenced to a minimum depth such that >80%% of targeted regions are sequenced to a depth greater than 20× reads.
Each purified amplicon library was sequenced to a minimum depth of 500 counts/strain/sample as described [ 18].
Genomes were sequenced to a mean coverage of 24.4×, with the minimum coverage of a sample being 14× and highest 64.7×.
For each sample, a minimum of 12 clones were sequenced, to determine the overall level of methylation within CpG islands.
The lower match for OncoSNP-SEQ is primarily due to our sample coverage being lower than that recommended for accurate OncoSNP-SEQ performance (our sample was sequenced to 30×, whereas OncoSNP-SEQ requires a minimum of 60×).
All private haplotypes were sequenced in a minimum of 2 independent runs in order to reduce the possibility of PCR artifacts.
Only unique DG sequences that were sequenced a minimum of three times and that mapped to a single location in the genome were used for genotyping.
Genes were sequenced from plasmids at a minimum of 4× coverage.
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