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Detailed information for vg0301117237:

Variant ID: vg0301117237 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1117237
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGAGTTTTTTTAGAACAGAGGGAGTAATTTGCTACTTTGGCATATAATTAAGGGAAAATTGCAAAAATCACCCCATAAGTCATTTGAAGTTTGACATT[C/T]
CACCCCATAAATTATTTTGTTGCAAATATCCACCCACCTACTCAATTTTGTTGCAAAAACCACCCCGGTAAACATATGCTTAACCGAATCAACATATTTT

Reverse complement sequence

AAAATATGTTGATTCGGTTAAGCATATGTTTACCGGGGTGGTTTTTGCAACAAAATTGAGTAGGTGGGTGGATATTTGCAACAAAATAATTTATGGGGTG[G/A]
AATGTCAAACTTCAAATGACTTATGGGGTGATTTTTGCAATTTTCCCTTAATTATATGCCAAAGTAGCAAATTACTCCCTCTGTTCTAAAAAAACTCTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.80% 14.00% 0.11% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 59.70% 40.10% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 80.80% 19.00% 0.13% 0.00% NA
Tropical Japonica  504 24.80% 74.80% 0.40% 0.00% NA
Japonica Intermediate  241 65.10% 34.40% 0.41% 0.00% NA
VI/Aromatic  96 70.80% 29.20% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg0301117237 C -> T LOC_Os03g02840.1 upstream_gene_variant ; 4192.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02840.4 upstream_gene_variant ; 4507.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02840.3 upstream_gene_variant ; 4242.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02840.2 upstream_gene_variant ; 4242.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02850.1 downstream_gene_variant ; 2507.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02850.2 downstream_gene_variant ; 2507.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301117237 C -> T LOC_Os03g02840-LOC_Os03g02850 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301117237 1.67E-08 NA mr1758_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
vg0301117237 NA 5.30E-08 mr1758_2 Jap_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