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. Author manuscript; available in PMC: 2020 Nov 28.
Published in final edited form as: Head Neck. 2019 Dec 18;42(4):688–697. doi: 10.1002/hed.26041

FIGURE 2.

FIGURE 2

HPV-16 DNA reads in each nucleotide position. Plots are shown for our cohort (A, C, D) and TCGA cohort (B). A, Average read counts at each HPV-16 nucleotide position in 40 samples. The HR density (over 25 000 reads) is observed at the junction between E5 and L2 regions (nucleotide position: 4189-4227). B, Average read counts at each HPV-16 nucleotide position in TCGA samples (N = 94). The HR density (>40 reads) is observed at the junction between E5 and L2 regions (nucleotide position: 4190-4261). C, Minimum read counts at each HPV-16 nucleotide position in all 40 samples. E1 specific region (nucleotide position: 1975-2195) contained the minimum read density across all samples. D, After exclusion of the lowest read sample data, minimum read counts replotted in each HPV-16 nucleotide position. Besides E1 specific region (BR E1; nucleotide position: 1975-2195), E6 specific region (BR E6; nucleotide position: 172-373) and the junction between E5 and L2 regions (HR E5L2; 4185-4334) contained the minimum read density across these 39 samples