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Table 5 Hits shared between CGH and coverage data using the Poisson-Gamma (PG) model, the FREEC software, and the cn.MOPS approach

From: A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

Strain Methodology Deletions Amplifications Overall
HB3 FREEC 195/210 (92.9%)
  cn.MOPS 214/348 (61.5%)
  PG with γ=99% 431/568 (75.9%)
  PG with γ=99.9% 288/365 (78.9%)
DD2 FREEC 792/831 (95.3%)
  cn.MOPS 746/840 (88.8%)
  PG with γ=99% 854/957 (89.0%)
  PG with γ=99.9% 826/899 (91.9%)
7G8 FREEC 89/154 (57.8%) 285/470 (60.6%) 374/624 (59.9%)
  cn.MOPS 91/477 (19.1%) 236/1185 (19.9%) 327/1662 (19.7%)
  PG with γ=99% 164/243 (67.5%) 216/343 (63.0%) 380/586 (64.9%)
  PG with γ=99.9% 153/205 (75.6%) 176/215 (81.9%) 329/420 (78.3%)
GB4 FREEC 32/82 (39.0%) 4/16 (25.0%) 36/98 (36.7%)
  cn.MOPS 77/197 (39.1%) 28/273 (10.3%) 105/470 (22.3%)
  PG with γ=99% 152/262 (59.0%) 24/108 (22.2%) 176/370 (47.6%)
  PG with γ=99.9% 148/253 (58.5%) 14/47 (29.8%) 162/300 (54.0%)
  1. CGH hits of HB3 and DD2 lab strains were taken from Samarakoon et al.[19], while CGH hits of 7G8 and GB4 lab strains were obtained by re-analysing the corresponding original data available from Jiang et al.[37]. The percentages in brackets are in relation to the total number of coverage hits produced by the corresponding method.