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Detailed information for vg0629028341:

Variant ID: vg0629028341 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29028341
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGATCGGCGACTGCTGCATCGACCTCTGCACGGACCCGCGCACGATGTTCTCGAGGTTCGGGCAGATGCTGGCGTAGTAGTTCTGCTTCAGCTGCGCC[A/G]
CCGCCAATGGCGACGAGATCGCCACCGCCAGCGCGAGGACGACGACGAAATGGAAGCTCCTCATCCTGTCGATGTTTTTCTCTTCACTACTTGAGCTTAA

Reverse complement sequence

TTAAGCTCAAGTAGTGAAGAGAAAAACATCGACAGGATGAGGAGCTTCCATTTCGTCGTCGTCCTCGCGCTGGCGGTGGCGATCTCGTCGCCATTGGCGG[T/C]
GGCGCAGCTGAAGCAGAACTACTACGCCAGCATCTGCCCGAACCTCGAGAACATCGTGCGCGGGTCCGTGCAGAGGTCGATGCAGCAGTCGCCGATCGCG

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 63.30% 36.70% 0.00% 0.00% NA
All Indica  2759 96.20% 3.80% 0.00% 0.00% NA
All Japonica  1512 4.40% 95.60% 0.00% 0.00% NA
Aus  269 45.00% 55.00% 0.00% 0.00% NA
Indica I  595 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 95.70% 4.30% 0.00% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 6.50% 93.50% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 64.40% 35.60% 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
vg0629028341 A -> G LOC_Os06g48010.1 missense_variant ; p.Val22Ala; MODERATE nonsynonymous_codon ; V22A Average:67.25; most accessible tissue: Minghui63 root, score: 85.77 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629028341 NA 3.17E-26 mr1251 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
vg0629028341 NA 2.44E-18 mr1253 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
vg0629028341 NA 6.50E-30 mr1257 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
vg0629028341 NA 2.20E-36 mr1435 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
vg0629028341 NA 1.01E-28 mr1638 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
vg0629028341 NA 7.55E-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
vg0629028341 NA 1.46E-57 mr1064_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
vg0629028341 NA 6.23E-38 mr1129_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
vg0629028341 NA 2.01E-23 mr1253_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