145 Molecular analysis for ovarian cancer detection in patient-friendly samples Supplemental Table 3: Shallow whole-genome sequencing coverage and quality statistics. Sample ID Library preparation Total number of sequenced reads Total number of uniquely mapped non-duplicate reads Total number of covered bases Median coverage per base Percentage of targeted bases with coverage ≥ 10X OC_feas_1 ThruPLEX Plasma-seq Kit (Takara Bio) 34443206 33229566 4600768397 1.0X 0.3% OC_feas_2 ThruPLEX Plasma-seq Kit (Takara Bio) 4841322 4534802 438559552 0.0X 0.1% OC_feas_3 ThruPLEX Plasma-seq Kit (Takara Bio) 8670936 8489020 551021318 1.0X 0.2% OC_feas_4 ThruPLEX Plasma-seq Kit (Takara Bio) 6622584 4903274 313628741 9.0X 48.7% OC_feas_5 ThruPLEX Plasma-seq Kit (Takara Bio) 3983596 3719015 212249544 0.0X 0.0% OC_feas_6 ThruPLEX Plasma-seq Kit (Takara Bio) 38765800 37853097 2052308677 0.0X 0.1% OC_feas_7 ThruPLEX Plasma-seq Kit (Takara Bio) 117445252 116737292 6597660157 0.0X 0.1% OC_feas_8 ThruPLEX Plasma-seq Kit (Takara Bio) 39243440 33682508 1942114454 0.0X 0.1% OC_feas_9 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 55213392 55133492 4817069501 2.0X 1.5% OC_feas_10 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 36361574 36295918 3146361198 1.0X 0.3% OC_feas_11 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 214080118 214025057 17885220140 7.0X 33.5% OC_feas_12 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 153789314 153494635 12073110695 5.0X 16.5% OC_feas_13 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 61933416 61703055 5195041255 2.0X 1.8% OC_feas_14 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 41047082 40545733 3625729946 1.0X 0.6% OC_feas_15 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 61948248 61749958 5148741517 2.0X 1.6% OC_feas_16 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 102101482 101856451 8564737514 3.0X 7.3% OC_feas_17 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 201244050 201125135 14932769622 6.0X 26.6% OC_feas_18 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 182260894 182096275 13778672708 6.0X 22.2% OC_feas_19 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 41249044 41097514 3636279625 1.7X 0.6% OC_feas_20 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 152163250 152091965 12414842765 5.9X 17.0% OC_feas_21 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 57461346 57378412 4707118763 2.2X 1.1% OC_feas_22 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 50560614 50490796 4565501330 2.2X 1.3% OC_feas_23 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 38128212 37980864 3460774777 1.7X 0.5% OC_feas_24 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 106041952 105808160 9403139563 4.5X 8.9% OC_feas_25 NEBNext® Enzymatic Methyl-seq (EM-seq) Kit 59473824 59277401 4954810846 2.4X 1.5% Trimmed non-converted and enzymatically converted reads were mapped to the GRCh38 human genome assembly (GeneBank accession: GCA_000001405.28). Targeted bases are defined as whole-genome. 5
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