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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1010572055:

Variant ID: vg1010572055 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10572055
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAATGTTAGTCTTCTTGGGAACAACCATGTGTATTGTGTTCTATAGCATAGCTAAGGTGGTGTTTGGATTCAGGGACTTAACTTTAGTCCCTATATTTA[A/G]
ACACTAATTTAGAGTATTAAATATAGACTACTTACAAAATTAATTACATAAATAAAAGCTAATTTGCGAGATAAATTTTTTAAGCCTAATTAATCTATAA

Reverse complement sequence

TTATAGATTAATTAGGCTTAAAAAATTTATCTCGCAAATTAGCTTTTATTTATGTAATTAATTTTGTAAGTAGTCTATATTTAATACTCTAAATTAGTGT[T/C]
TAAATATAGGGACTAAAGTTAAGTCCCTGAATCCAAACACCACCTTAGCTATGCTATAGAACACAATACACATGGTTGTTCCCAAGAAGACTAACATTTG

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 17.90% 6.50% 2.94% 72.68% NA
All Indica  2759 1.70% 0.30% 3.33% 94.71% NA
All Japonica  1512 49.90% 19.00% 2.12% 28.97% NA
Aus  269 1.10% 0.00% 2.60% 96.28% NA
Indica I  595 1.00% 0.20% 3.70% 95.13% NA
Indica II  465 1.70% 0.20% 4.52% 93.55% NA
Indica III  913 1.50% 0.40% 1.97% 96.06% NA
Indica Intermediate  786 2.40% 0.10% 3.94% 93.51% NA
Temperate Japonica  767 61.30% 28.80% 3.26% 6.65% NA
Tropical Japonica  504 43.70% 4.40% 0.20% 51.79% NA
Japonica Intermediate  241 27.00% 18.30% 2.49% 52.28% NA
VI/Aromatic  96 12.50% 5.20% 3.12% 79.17% NA
Intermediate  90 33.30% 6.70% 5.56% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1010572055 A -> G LOC_Os10g20870.1 downstream_gene_variant ; 2945.0bp to feature; MODIFIER silent_mutation Average:43.884; most accessible tissue: Callus, score: 95.98 N N N N
vg1010572055 A -> G LOC_Os10g20860.1 intron_variant ; MODIFIER silent_mutation Average:43.884; most accessible tissue: Callus, score: 95.98 N N N N
vg1010572055 A -> DEL N N silent_mutation Average:43.884; most accessible tissue: Callus, score: 95.98 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010572055 NA 2.24E-06 mr1041_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
vg1010572055 NA 2.39E-06 mr1184_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
vg1010572055 NA 3.94E-06 mr1278_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
vg1010572055 NA 1.69E-06 mr1293_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
vg1010572055 2.94E-06 2.94E-06 mr1371_2 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
vg1010572055 4.65E-06 NA mr1417_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
vg1010572055 5.94E-06 4.42E-06 mr1417_2 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
vg1010572055 NA 7.47E-06 mr1508_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
vg1010572055 8.88E-06 2.79E-06 mr1556_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
vg1010572055 4.04E-06 NA mr1645_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
vg1010572055 6.00E-07 NA mr1647_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
vg1010572055 2.96E-06 2.96E-06 mr1647_2 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
vg1010572055 7.43E-06 NA mr1648_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
vg1010572055 9.44E-06 9.44E-06 mr1648_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
vg1010572055 8.64E-06 NA mr1672_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
vg1010572055 2.46E-06 NA mr1840_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
vg1010572055 9.05E-06 1.09E-07 mr1992_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