2015 BOSC panelists (from left): Michael R. Crusoe, Holly Bik, Jason Williams, and Aleksandra Pawlik.

<p>2015 BOSC panelists (from left): Michael R. Crusoe, Holly Bik, Jason Williams, and Aleksandra Pawlik.</p

Additional file 9: Figure S5. of Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities

MAF distribution for SNVs in the 1000 Genomes Project but not in this study. (DOCX 49 kb

Performance of Illumina and 454 sequencing for the detection of amino acid minority variants within the control library.

<p>Expected variant percentages include positions where a MV is present on more than one clone. Median variant % reflects only the minority variants detected by each platform and does not include the undetected variants. N represents the number of nucleotide positions in the control library where the variant frequency is expected. Illumina detected 1 false positive minority variant present at 0.7% of the viral population and 454 detected 5 false positive minority variants ranging from 0.09% to 0.6%. FN, false negative.</p

Effect of down-sampling Illumina coverage on true positive and false positive rates.

<p>Plots are of the median true positive and false positive minority variant detection rates of the control library with the standard deviation shown as error bars from 10 iterations of random sampling from all reads to generate each coverage depth.</p

Measured versus expected minority variant percentages detected in the control library by Illumina and 454 sequencing.

<p>(A) Nucleotide percentages are plotted with linear regression line and 95% confidence intervals. (B) Amino acid percentages are plotted with 95% confidence intervals. MV, minority variant.</p

Minority variants detected by Illumina and/or 454 sequencing in the 5 patient samples combined.

<p>(A) Nucleotide minority variants categorized by platform (Illumina vs. 454) and whether the minority variants were detected by both Illumina and 454 or by one platform only. The “Illumina (w/454)” category refers to the Illumina minority variant calls that are also detected by 454 and the “454 (w/Illumina)” category refers to the 454 calls that are also detected by Illumina. (B) Pearson correlation of the nucleotide minority variants detected by both Illumina and 454. (C) Amino acid minority variants categorized by platform and whether the variants were detected by both Illumina and 454 or by one platform only. (D) Pearson correlation of the amino acid minority variants detected by both Illumina and 454. MV, minority variant.</p