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Table 1 Total number of variants in 1779 individuals by MAF and functional category

From: NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Type Frequencya Number of variants Functional variation
Protein coding region Non-coding region
Silent/nonframeshift Missense/frameshift Stoploss/Stopgain Unknown Intronic Intergenic Splicing UTR ncRNA
SNP Singleton 17,811,366 86,804 146,480 3722 2690 6,842,300 9,370,754 2110 247,422 1,109,084
Rare 13,673,626 54,642 87,791 1658 1917 5,270,353 7,248,270 1363 164,492 843,140
Low 3,430,315 12,753 15,710 232 428 1,299,727 1,851,373 245 38,673 211,174
Common 5,727,339 17,886 15,981 151 729 2,049,372 3,228,994 159 53,221 360,846
Total 40,642,646 172,085 265,962 5763 5764 15,461,752 21,699,391 3877 503,808 2,524,244
Indel Singleton 1,402,707 3191 5068 157 129 558,772 717,182 517 27,748 89,943
Rare 1,376,996 2733 2884 127 127 544,183 717,045 217 22,047 87,633
Low 452,337 634 827 37 37 173,946 241,506 61 6444 28,845
Common 569,436 422 369 18 89 207,132 317,135 145 7157 36,969
Total 3,801,476 6980 9148 339 382 1,484,033 1,992,868 940 63,396 243,390
  1. aRare, MAF < 0.5%; low, 0.5% ≤ MAF < 5%; common, MAF ≥ 5%