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Detailed information for vg0614104820:

Variant ID: vg0614104820 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 14104820
Reference Allele: TCCGAlternative Allele: CCCG,T
Primary Allele: TCCGSecondary Allele: CCCG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGCAGGTTACAGTTGATCCGAGCGAAGAGGTTGATGGCTTGCCGAGGCTGGTCCTCCTTGAGGGAATGAACAGTAAGACTGCTCTTTTCGCTACAAGCT[TCCG/CCCG,T]
TGCTTTTGCTATTTTGCTTTATTTGACTTTTGACATGACTCCCCCTTGCCTTTACAGTGCTAACCCTCGACCAAGCTGAAGCCGAAGCCCGCAAGATGAT

Reverse complement sequence

ATCATCTTGCGGGCTTCGGCTTCAGCTTGGTCGAGGGTTAGCACTGTAAAGGCAAGGGGGAGTCATGTCAAAAGTCAAATAAAGCAAAATAGCAAAAGCA[CGGA/CGGG,A]
AGCTTGTAGCGAAAAGAGCAGTCTTACTGTTCATTCCCTCAAGGAGGACCAGCCTCGGCAAGCCATCAACCTCTTCGCTCGGATCAACTGTAACCTGCCA

Allele Frequencies:

Populations Population SizeFrequency of TCCG(primary allele) Frequency of CCCG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.60% 12.30% 6.86% 15.00% T: 0.21%
All Indica  2759 48.90% 18.10% 10.58% 22.04% T: 0.36%
All Japonica  1512 97.40% 0.20% 0.66% 1.79% NA
Aus  269 75.10% 0.70% 3.35% 20.82% NA
Indica I  595 24.00% 11.10% 13.95% 50.25% T: 0.67%
Indica II  465 25.20% 40.40% 17.85% 16.34% T: 0.22%
Indica III  913 79.40% 7.70% 4.71% 8.00% T: 0.22%
Indica Intermediate  786 46.30% 22.40% 10.56% 20.36% T: 0.38%
Temperate Japonica  767 96.20% 0.00% 1.30% 2.48% NA
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 96.70% 1.20% 0.00% 2.07% NA
VI/Aromatic  96 14.60% 75.00% 7.29% 3.12% NA
Intermediate  90 71.10% 5.60% 6.67% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614104820 TCCG -> T LOC_Os06g24090.1 upstream_gene_variant ; 3809.0bp to feature; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> T LOC_Os06g24110.1 downstream_gene_variant ; 2410.0bp to feature; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> T LOC_Os06g24100.1 intron_variant ; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> DEL N N silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> CCCG LOC_Os06g24090.1 upstream_gene_variant ; 3808.0bp to feature; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> CCCG LOC_Os06g24110.1 downstream_gene_variant ; 2411.0bp to feature; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0614104820 TCCG -> CCCG LOC_Os06g24100.1 intron_variant ; MODIFIER silent_mutation Average:43.19; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614104820 2.77E-08 NA mr1632_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0614104820 4.11E-06 NA mr1632_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251