Table 1.
Comparison of AMYCNE, DCNE of AMY1, and CNVnator against the AMY1 ddPCR measurements.
Fig 1.
A comparison of three WGS copy number estimation methods.
A comparison of the three WGS copy number estimation methods: (a) AMYCNE, (b) Diploid copy number estimation of AMY1, and (c) CNVnator. In all heat maps the number of samples per point is illustrated by color from red (low numbers) to blue (high numbers) as shown in the color key.
Fig 2.
The precision of AMYCNE and ddPCR measurements.
A comparison of the length of confidence intervals and copy number reported by AMYCNE and ddPCR in red and blue respectively.
Fig 3.
Copy number distributions of the AMY genes.
Histograms of the copy number distributions of the three genes in the AMY locus: (a) AMY1, (b) AMY2A and (c) AMY2B.
Fig 4.
Patterns of the AMY gene copy numbers.
(a) A score plot of the copy number distribution of the AMY genes. Each dot is colored according to the AMY1 copy number of that sample. (b) A scatter plot of the AMY2A copy number versus the AMY1 copy number. The dots are colored according to the number of samples having each combination of AMY2A and AMY1 copy numbers.
Table 2.
Comparison of AMYCNE and CNVnator against the truth-set presented in [16].
Fig 5.
Copy number predictions of mosaic aneuploidies of chromosome X.
The predicted X chromosome copy number plotted against the true copy number. The results of the three copy number prediction software are presented in three different colors: red (AMYCNE), green (CNVnator), and blue (Raw coverage estimation).
Table 3.
Precision and sensitivity of Delly on the NA12878 sample, using various combinations of filters.