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Detailed information for vg0818318988:

Variant ID: vg0818318988 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18318988
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTCTTTTTCTAAAAGGCTGTAGACCTGTGTATATCACGTACTTTTTTTTAGAAATAATACGTGCACACTTTATCTCTATAAATGCATCTGGACACCCT[G/A]
TTACGAGCACTTTCGAAACACTAAAAGACTAGATCGACATATTTTTTTTGAGATTAACGAAGTTACTACGGGCGCTTCATTTGAAAATGTTAGCTACAAA

Reverse complement sequence

TTTGTAGCTAACATTTTCAAATGAAGCGCCCGTAGTAACTTCGTTAATCTCAAAAAAAATATGTCGATCTAGTCTTTTAGTGTTTCGAAAGTGCTCGTAA[C/T]
AGGGTGTCCAGATGCATTTATAGAGATAAAGTGTGCACGTATTATTTCTAAAAAAAAGTACGTGATATACACAGGTCTACAGCCTTTTAGAAAAAGAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.10% 5.70% 0.66% 7.60% NA
All Indica  2759 89.20% 4.00% 0.14% 6.74% NA
All Japonica  1512 85.30% 2.20% 1.46% 10.98% NA
Aus  269 56.10% 41.30% 1.49% 1.12% NA
Indica I  595 76.50% 0.20% 0.50% 22.86% NA
Indica II  465 92.90% 4.30% 0.00% 2.80% NA
Indica III  913 93.90% 5.80% 0.00% 0.33% NA
Indica Intermediate  786 91.10% 4.50% 0.13% 4.33% NA
Temperate Japonica  767 98.20% 0.80% 0.39% 0.65% NA
Tropical Japonica  504 72.00% 0.60% 3.17% 24.21% NA
Japonica Intermediate  241 72.20% 10.40% 1.24% 16.18% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 86.70% 7.80% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818318988 G -> A LOC_Os08g29790.1 upstream_gene_variant ; 4934.0bp to feature; MODIFIER silent_mutation Average:42.624; most accessible tissue: Minghui63 flower, score: 59.225 N N N N
vg0818318988 G -> A LOC_Os08g29809.1 downstream_gene_variant ; 101.0bp to feature; MODIFIER silent_mutation Average:42.624; most accessible tissue: Minghui63 flower, score: 59.225 N N N N
vg0818318988 G -> A LOC_Os08g29790-LOC_Os08g29809 intergenic_region ; MODIFIER silent_mutation Average:42.624; most accessible tissue: Minghui63 flower, score: 59.225 N N N N
vg0818318988 G -> DEL N N silent_mutation Average:42.624; most accessible tissue: Minghui63 flower, score: 59.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818318988 2.14E-06 3.69E-07 mr1040 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
vg0818318988 2.86E-06 1.06E-09 mr1836 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251