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Detailed information for vg0307639490:

Variant ID: vg0307639490 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7639490
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGTCAAAAAGGCAAGGTGTGCAAATTGTTGAAGTCTTTGTATGGTCTGAAACAAGCTCCTAAGCAATGGCATGAGAAATTTGACAAGACATTGACATCT[A/G]
CAGGCTTCGCAGTCAATGAGGCAGATAAATGTGTGTACTATCGCTATGGTGGGGGTGAGGGAGTTATTTTATGCTTGTATGTTGATGACATACTGATATT

Reverse complement sequence

AATATCAGTATGTCATCAACATACAAGCATAAAATAACTCCCTCACCCCCACCATAGCGATAGTACACACATTTATCTGCCTCATTGACTGCGAAGCCTG[T/C]
AGATGTCAATGTCTTGTCAAATTTCTCATGCCATTGCTTAGGAGCTTGTTTCAGACCATACAAAGACTTCAACAATTTGCACACCTTGCCTTTTTGACCT

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 72.50% 27.40% 0.06% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 17.10% 82.90% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 19.90% 80.10% 0.00% 0.00% NA
Tropical Japonica  504 18.50% 81.30% 0.20% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 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
vg0307639490 A -> G LOC_Os03g14060.1 missense_variant ; p.Thr856Ala; MODERATE nonsynonymous_codon ; T856A Average:8.59; most accessible tissue: Callus, score: 22.943 benign -0.591 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307639490 NA 1.21E-18 Yield All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0307639490 NA 5.79E-16 mr1062 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
vg0307639490 NA 3.44E-09 mr1198 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
vg0307639490 1.65E-07 NA mr1403 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
vg0307639490 NA 4.02E-07 mr1453 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
vg0307639490 NA 9.88E-06 mr1516 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
vg0307639490 NA 2.58E-06 mr1646 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
vg0307639490 NA 9.00E-11 mr1683 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
vg0307639490 NA 2.90E-19 mr1715 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
vg0307639490 NA 1.87E-07 mr1779 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
vg0307639490 NA 1.81E-16 mr1968 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