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Detailed information for vg0630884821:

Variant ID: vg0630884821 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30884821
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGAGTAGAGAATCTACATCAATTTTCTCGTGAAACTATGTGTAGACCTTCCCCATTCAAATAACAATAATCTTCACCAACAAAAAGTCATGTAACCTA[G/A]
TGGTTACAGTGACCTGAGTAGTACCTCAAAGTTCTGAGTTTAAATCTTCTATGGAGCGAATTTTAGATTGAGTTAGATTGAGTTGTTTACGGGGCTAAGT

Reverse complement sequence

ACTTAGCCCCGTAAACAACTCAATCTAACTCAATCTAAAATTCGCTCCATAGAAGATTTAAACTCAGAACTTTGAGGTACTACTCAGGTCACTGTAACCA[C/T]
TAGGTTACATGACTTTTTGTTGGTGAAGATTATTGTTATTTGAATGGGGAAGGTCTACACATAGTTTCACGAGAAAATTGATGTAGATTCTCTACTCCAA

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 95.50% 4.50% 0.04% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 88.10% 11.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 85.70% 14.30% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 75.90% 24.10% 0.00% 0.00% NA
VI/Aromatic  96 68.80% 30.20% 1.04% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0630884821 G -> A LOC_Os06g51050.1 upstream_gene_variant ; 2394.0bp to feature; MODIFIER silent_mutation Average:36.875; most accessible tissue: Callus, score: 77.415 N N N N
vg0630884821 G -> A LOC_Os06g51029-LOC_Os06g51050 intergenic_region ; MODIFIER silent_mutation Average:36.875; most accessible tissue: Callus, score: 77.415 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630884821 1.36E-06 NA mr1252 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
vg0630884821 NA 3.25E-07 mr1278 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
vg0630884821 NA 3.74E-06 mr1293 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
vg0630884821 NA 3.08E-06 mr1681 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
vg0630884821 NA 4.11E-07 mr1824 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
vg0630884821 NA 9.14E-06 mr1221_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