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Detailed information for vg0629489803:

Variant ID: vg0629489803 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29489803
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTCATACAGAGCTAGAGTTAAGTTAATATATAAATTATAGACCTAAAGGCTCGTGATCAATGCCCTTCGCCACCTCTAAAGTTAGTCATATGGATATC[G/A]
ATTTCGCAAGCCTTACTTATTAGGGCCGACACATGGCTAAACCAAGTGATGTTGGGTCTGTTCGGCTGTCTGTTTCGTGGTTGCGGCGTAACCAGCACCA

Reverse complement sequence

TGGTGCTGGTTACGCCGCAACCACGAAACAGACAGCCGAACAGACCCAACATCACTTGGTTTAGCCATGTGTCGGCCCTAATAAGTAAGGCTTGCGAAAT[C/T]
GATATCCATATGACTAACTTTAGAGGTGGCGAAGGGCATTGATCACGAGCCTTTAGGTCTATAATTTATATATTAACTTAACTCTAGCTCTGTATGAAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.80% 34.60% 0.21% 1.42% NA
All Indica  2759 89.60% 8.20% 0.22% 1.99% NA
All Japonica  1512 17.20% 82.10% 0.07% 0.66% NA
Aus  269 54.60% 45.40% 0.00% 0.00% NA
Indica I  595 86.20% 10.60% 0.17% 3.03% NA
Indica II  465 94.60% 2.60% 0.22% 2.58% NA
Indica III  913 89.90% 8.40% 0.22% 1.42% NA
Indica Intermediate  786 88.70% 9.50% 0.25% 1.53% NA
Temperate Japonica  767 4.00% 95.70% 0.00% 0.26% NA
Tropical Japonica  504 27.80% 70.60% 0.20% 1.39% NA
Japonica Intermediate  241 36.90% 62.70% 0.00% 0.41% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 54.40% 40.00% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0629489803 G -> A LOC_Os06g48720-LOC_Os06g48730 intergenic_region ; MODIFIER silent_mutation Average:37.95; most accessible tissue: Callus, score: 86.205 N N N N
vg0629489803 G -> DEL N N silent_mutation Average:37.95; most accessible tissue: Callus, score: 86.205 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629489803 NA 9.46E-17 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
vg0629489803 NA 7.30E-06 mr1992 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
vg0629489803 NA 7.86E-12 mr1660_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
vg0629489803 NA 1.62E-11 mr1714_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
vg0629489803 NA 1.06E-11 mr1781_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
vg0629489803 NA 8.24E-11 mr1806_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
vg0629489803 NA 2.49E-21 mr1968_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