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Table 2 General characteristics of the common, rare and novel single nucleotide variations (SNVs)

From: Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

Total number (average per sample) All Common Rare Novela
All (Immunoseq) 351,088 (90,594) 275,042 (83,839) 50,004 (5318) 26,042 (1437)
Codingb All 60,946 (15,169) 45,545 (1818) 12,452 (1166) 2949 (185)
Non-synonymousc 30,967 (7174) 21,807 (6403) 7405 (669) 1755 (102)
Synonymousc 29,214 (7770) 23,434 (7305) 4785 (395) 995 (71)
Stop-gainedc 395 (71) 202 (56) 135 (13) 58 (2)
Exomed 120,245 (30,682) 91,818 (27,916) 21,497 (2280) 6930 (486)
Non-codinge 290,142 (75,424) 229,497 (70,020) 37,552 (4152) 23,093 (1251)
All DHSf 195,182 (51,559) 154,154 (48,056) 24,571 (2677) 16,457 (826)
  1. Total number of variants and the average number of variants per sample that were included in the Immunoseq design
  2. aNovel variants are defined as not identified in the 1000 Genomes Project nor included in dbSNP141. bCoding variants are those located in the exons of the RefSeq coding sequence. cSynonymous, non-synonymous and stop-gained variants were annotated using SNPeff and the hg19 version of the genome. dThe Exome is based on the Roche SeqCap EZ exome v3.0. e Non-coding variants are those not in the RefSeq coding sequence. f The All DHSs category combines all DHSs from the selected 12 cell types and could partly overlap with the Exome. Cut-offs used for the quality control of the variants are read depth ≥ 10, genotyping quality (gq) ≥ 70, mapping quality (MQ) ≥50, and proportion of the reference allele between 10 and 90 %