Reading zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf Reading zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-results.vcf sample_number CpGsWithSNP sampleID SNPsAll SNPsPASS CTorGA heterozygous 1 1 66019 2H-1 2151529 1269252 228635 730979 2 2 69666 2H-2 2244580 1361903 244356 789338 3 3 51083 2H-3 1923149 1021426 159145 673664 4 4 65692 2H-4 2179427 1291185 218552 853207 5 5 59230 2H-5 2062090 1165921 192188 762470 6 6 71854 2H-6 2269174 1398573 246915 930420 7 7 104628 2L-1 2820291 1989062 393304 1352110 8 8 56254 2L-2 1998275 1103556 180633 718784 9 9 63228 2L-3 2094821 1208703 205658 798217 10 10 69835 2L-4 2221917 1345565 235386 887430 11 11 75878 2L-5 2331291 1458307 259883 973120 12 12 62272 2L-6 2140551 1252727 204948 821845 13 13 72220 3H-1 2277569 1401813 246901 932642 14 14 47526 3H-2 1859380 944499 151564 531488 15 15 77846 3H-3 2378434 1513818 273690 1005130 16 16 67579 3H-4 2172435 1298292 226416 859148 17 17 72553 3H-5 2258967 1383046 256030 804207 18 18 70940 3H-6 2214733 1349020 241563 903578 19 19 66646 3L-1 2169998 1291498 224411 861185 20 20 69592 3L-2 2231861 1344124 236223 893540 21 21 68276 3L-3 2205404 1320880 229631 871477 22 22 65009 3L-4 2117457 1242104 217533 818436 23 23 53645 3L-5 1942310 1049730 170559 686050 24 24 71258 3L-6 2234822 1367245 245768 906239 424005 of 12794074 covered CpGs have a PASS SNP at the C or G in at least one sample R version 4.4.3 (2025-02-28) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 24.04.4 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 locale: [1] C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] data.table_1.17.0 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 [5] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 [9] tibble_3.2.1 ggplot2_3.5.2 tidyverse_2.0.0 loaded via a namespace (and not attached): [1] bit_4.6.0 gtable_0.3.6 compiler_4.4.3 crayon_1.5.3 [5] tidyselect_1.2.1 parallel_4.4.3 scales_1.3.0 R6_2.6.1 [9] generics_0.1.3 munsell_0.5.1 pillar_1.10.2 tzdb_0.5.0 [13] rlang_1.1.5 stringi_1.8.7 bit64_4.6.0-1 timechange_0.3.0 [17] cli_3.6.4 withr_3.0.2 magrittr_2.0.3 grid_4.4.3 [21] vroom_1.6.5 hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5 [25] glue_1.8.0 colorspace_2.1-1 tools_4.4.3 pkgconfig_2.0.3