Tumor ploidy estimates. Panels labelled as SAVANA-paired germline SNPs show results for matched tumor-normal pair analysis using matched normal germline SNPs for purity estimation. Panels labelled as SAVANA-paired 1000 G SNPs show results for matched tumor-normal pair analysis using the 1000 Genome Project population SNPs with allele fractions >0.25 and allele fractions <0.75. Panels labelled as The SAVANA tumor-only 1000 G SNPs show results for analysis using the 1000 Genome Project population SNPs with allele fractions >0.25 and allele fractions <0.75. For this analysis, we only considered the 44 tumors with region-matched nanopore and Illumina WGS data. *** P < 0.0001. The P values for tumor ploidy comparisons depicted in b were P < 2.2 x 10 -16, P < 2.2 x 10 -16, P = 2.6 x 10 -16, P < 2.2 x 10 -16, P = 1.1 x 10 -13 and P <= 1.9 x 10 -12, respectively (reading from top to bottom, left to right).
