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Table 1 Sensitivity of assignment to somatic single nucleotide variant groups on simulated data

From: Fast and scalable inference of multi-sample cancer lineages

  Coverage   
Number of Number of True VAF 10,000 × 1,000 × 100 ×
samples simulated SSNVs (+CNV) (+CNV) (+CNV) (+CNV)
5 26.6 (42.2) 99.2 (96.9) 98.9 (96.7) 99.1 (96.7) 97.2 (95.5)
  25 (44.5) 99.5 (97.4) 99.1 (97.3) 99.3 (97.4) 97.4 (95.9)
10 43.9 (89.7) 99.2 (97.8) 98.5 (97.5) 98.5 (97.7) 95 (96)
  40.7 (88.6) 99.5 (97.5) 99.1 (97.3) 99 (97.3) 96.3 (95.9)
15 53.6 (131.1) 98.8 (96.9) 98.2 (96.7) 97.9 (96.5) 94.2 (95.4)
  51 (136.1) 99.1 (97.6) 98.7 (97.4) 98.5 (97.2) 94.5 (95.8)
  1. Values indicate the number of correctly assigned SSNVs out of the total number of SSNVs collected in each experiment (number of simulated SSNVs). Results are shown for 5, 10, and 15 samples given true VAFs, 10,000 ×, 1,000 ×, and 100 × coverage data obtained with localized (top row in each pair) and randomized (bottom row) sampling, from trees without CNVs and with approximately 80% of SSNVs in CNV regions (in parentheses). All values are averaged over 100 simulated trees. CNV, copy number variant; SSNV, somatic single nucleotide variant; VAF, variant allele frequency.