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Detailed information for vg0819407985:

Variant ID: vg0819407985 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19407985
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCCAAGCCGATGCGGATGTTGGTTCTTGGTCTGGAGCAAGCGATATGCCTCGCTACTAGCTCTGGACTCGGGGGTCGACTTCTTCGCATGGAATTCCTC[T/C]
CAGACCTGTTTCGTGATCCAAGGAAATTTCTCTCTTGGATCTAGATTCGCCGGGTTGTAGACGAACTCGCCGACTAGCTTAGTCTTGAAGTTCTTCCAAG

Reverse complement sequence

CTTGGAAGAACTTCAAGACTAAGCTAGTCGGCGAGTTCGTCTACAACCCGGCGAATCTAGATCCAAGAGAGAAATTTCCTTGGATCACGAAACAGGTCTG[A/G]
GAGGAATTCCATGCGAAGAAGTCGACCCCCGAGTCCAGAGCTAGTAGCGAGGCATATCGCTTGCTCCAGACCAAGAACCAACATCCGCATCGGCTTGGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.40% 0.22% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0819407985 T -> C LOC_Os08g31390.1 splice_region_variant&intron_variant ; LOW N Average:21.967; most accessible tissue: Callus, score: 30.966 N N N N
vg0819407985 T -> C LOC_Os08g31380.1 upstream_gene_variant ; 2755.0bp to feature; MODIFIER N Average:21.967; most accessible tissue: Callus, score: 30.966 N N N N
vg0819407985 T -> C LOC_Os08g31400.1 downstream_gene_variant ; 3331.0bp to feature; MODIFIER N Average:21.967; most accessible tissue: Callus, score: 30.966 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819407985 4.73E-06 1.74E-08 mr1278 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
vg0819407985 NA 9.52E-06 mr1538 Ind_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
vg0819407985 8.20E-06 8.16E-06 mr1954 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