Table 2.
Potential mosaic mutations
| Child | ID | HiFi | HiFi AB | ONT | ONT AB | Illumina | Illumina AB | Parental haplotype |
|---|---|---|---|---|---|---|---|---|
| 14455.p1 | chr2_94618830_C_A | 3/48 | 0.06 | 2/14 | 0.14 | 1/66 | 0.02 | paternal hap1 |
| 14455.p1 | chr4_1518905_G_C | 5/16 | 0.31 | 2/13 | 0.15 | 1/25 | 0.04 | maternal hap1 |
| 14455.p1 | chr5_124981762_T_C | 12/54 | 0.22 | 2/16 | 0.13 | 6/64 | 0.09 | maternal hap1 |
| 14455.p1 | chr9_42454095_C_T | 4/33 | 0.12 | 3/9 | 0.33 | 1/37 | 0.03 | maternal hap2 |
| 14455.p1 | chr17_81586404_G_C | 3/24 | 0.13 | 3/22 | 0.14 | 8/43 | 0.19 | maternal hap1 |
| 14455.p1 | chr18_15654268_G_T | 8/40 | 0.20 | 2/21 | 0.10 | 1/62 | 0.02 | paternal hap2 |
| 14455.p1 | chrX_114777954_G_A | 3/31 | 0.10 | 3/26 | 0.12 | 1/40 | 0.03 | maternal hap1 |
| 14455.s1 | chr1_2104522_A_G | 2/20 | 0.10 | 1/26 | 0.04 | 0/23 | 0.00 | paternal hap2 |
| 14455.s1 | chr2_91095600_G_T | 3/30 | 0.10 | 2/14 | 0.14 | 2/126 | 0.02 | maternal hap1 |
| 14455.s1 | chr3_96412796_A_C | 2/33 | 0.06 | 1/40 | 0.03 | 0/34 | 0.00 | maternal hap1 |
| 14455.s1 | chr6_62484584_G_A | 6/34 | 0.18 | 3/24 | 0.13 | 1/39 | 0.03 | maternal hap2 |
| 14455.s1 | chr6_70745885_CAT_C | 4/22 | 0.18 | 2/31 | 0.06 | 1/7 | 0.14 | unknown |
| 14455.s1 | chr6_127695258_G_A | 5/35 | 0.14 | 1/35 | 0.03 | 2/32 | 0.06 | paternal hap2 |
| 14455.s1 | chr6_163529274_T_C | 4/28 | 0.14 | 2/28 | 0.07 | 2/15 | 0.13 | maternal hap1 |
| 14455.s1 | chr7_2981075_TATATAG_T | 6/30 | 0.20 | 1/39 | 0.03 | 1/36 | 0.03 | maternal hap1 |
| 14455.s1 | chr7_58404995_T_A | 4/30 | 0.13 | 1/29 | 0.03 | 1/50 | 0.02 | paternal hap2 |
| 14455.s1 | chr7_58405316_C_T | 4/31 | 0.13 | 1/27 | 0.04 | 1/56 | 0.02 | paternal hap2 |
| 14455.s1 | chr7_156505941_C_A | 2/30 | 0.07 | 1/29 | 0.03 | 3/22 | 0.14 | unknown |
| 14455.s1 | chr11_50917416_C_A | 3/28 | 0.11 | 5/17 | 0.29 | 1/28 | 0.04 | paternal hap1 |
| 14455.s1 | chr14_3924466_C_CATTCCATTCCATTCT | 1/23 | 0.04 | 2/3 | 0.67 | 1/54 | 0.02 | unknown |
| 14455.s1 | chr14_10160460_G_Ta | 3/29 | 0.10 | 1/15 | 0.07 | 1/13 | 0.08 | maternal hap2 |
| 14455.s1 | chr19_5409128_C_T | 6/33 | 0.18 | 1/26 | 0.04 | 8/55 | 0.15 | paternal hap1 |
| 14455.s1 | chr22_20777172_G_Ta | 8/42 | 0.19 | 1/27 | 0.04 | 1/62 | 0.02 | maternal hap2 |
DNMs identified after removing the allele balance filter for HiFi long-read data aligned to T2T-CHM13. The number of reads with the alternate allele, total number of reads, and allele balance (AB) ratio for PacBio HiFi, ONT, and Illumina.
a
All variants were identified by GATK with the exception of the two variants identified by DeepVariant, denoted with the superscript.