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Detailed information for vg0307900638:

Variant ID: vg0307900638 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7900638
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGAAATATAAGTTTTTTATAAAAGGATCAACATGTAAAACATGCAGGCTTTAGGTGTGTTTAGTTTACGCCAAAATTGAGATTTTGGTTGAAAATGGAA[C/T]
GATGCAACAGAAAAATTAAAAATTTGTGTGTAGAAAAGTTTTGATGTGATGAAAAAGTTAAAAGTTTGGAAGTAAACTCGGCCTTTCTTCTACCCACGTA

Reverse complement sequence

TACGTGGGTAGAAGAAAGGCCGAGTTTACTTCCAAACTTTTAACTTTTTCATCACATCAAAACTTTTCTACACACAAATTTTTAATTTTTCTGTTGCATC[G/A]
TTCCATTTTCAACCAAAATCTCAATTTTGGCGTAAACTAAACACACCTAAAGCCTGCATGTTTTACATGTTGATCCTTTTATAAAAAACTTATATTTCAT

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 82.50% 17.50% 0.04% 0.00% NA
All Indica  2759 84.80% 15.20% 0.07% 0.00% NA
All Japonica  1512 80.60% 19.40% 0.00% 0.00% NA
Aus  269 88.80% 11.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 69.30% 30.60% 0.11% 0.00% NA
Indica Intermediate  786 84.20% 15.60% 0.13% 0.00% NA
Temperate Japonica  767 83.60% 16.40% 0.00% 0.00% NA
Tropical Japonica  504 70.80% 29.20% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0307900638 C -> T LOC_Os03g14550.1 downstream_gene_variant ; 4755.0bp to feature; MODIFIER silent_mutation Average:62.592; most accessible tissue: Zhenshan97 panicle, score: 88.062 N N N N
vg0307900638 C -> T LOC_Os03g14560.1 intron_variant ; MODIFIER silent_mutation Average:62.592; most accessible tissue: Zhenshan97 panicle, score: 88.062 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307900638 NA 7.61E-07 mr1027 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
vg0307900638 1.46E-06 9.84E-08 mr1830 Jap_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
vg0307900638 NA 2.29E-06 mr1027_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
vg0307900638 NA 4.11E-06 mr1831_2 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
vg0307900638 NA 8.02E-07 mr1840_2 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