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Table 3 SnpEff sanity check of hg19, hg19K and hg19KIndel

From: hg19KIndel: ethnicity normalized human reference genome

Sanity Check while building compatible snpEff database

Genome

Compatible annotation database

Reference mRNA

Match percentage between the respective genome and refSeq

Protein level

mRNA level

Existing baseline

hg19

refGene

refSeq

92.81

95.2

After replacing only minor SNP alleles with major alleles in hg19

hg19K

refGene

refSeq

85.79

70.48

After to replacing minor INDELS with major alleles in hg19K

hg19KIndel

refGeneKINDEL

refSeq

85.75

69.96