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Detailed information for vg1012708940:

Variant ID: vg1012708940 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12708940
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGCAGTTCAGTGTTGATTAAAATTGATGATTACTCTATTGTTTTACTATTCTTAAATATTTGCTAAATGCTGATTTTGCAAATGAGCCTATATTATGC[C/T]
ATCCTTTGGTATCCTTGTGCACTTGCATATTTGCTGTGTGGCTTGAGTATTTCATATGCTCATTCTTGCAATAATCAATCAACCTCAGTTGAAGAAAAAG

Reverse complement sequence

CTTTTTCTTCAACTGAGGTTGATTGATTATTGCAAGAATGAGCATATGAAATACTCAAGCCACACAGCAAATATGCAAGTGCACAAGGATACCAAAGGAT[G/A]
GCATAATATAGGCTCATTTGCAAAATCAGCATTTAGCAAATATTTAAGAATAGTAAAACAATAGAGTAATCATCAATTTTAATCAACACTGAACTGCACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.20% 0.40% 0.21% 0.17% NA
All Indica  2759 99.70% 0.00% 0.04% 0.29% NA
All Japonica  1512 98.20% 1.30% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.20% 0.00% 0.00% 0.77% NA
Indica Intermediate  786 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 96.60% 2.50% 0.91% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg1012708940 C -> T LOC_Os10g24720.1 upstream_gene_variant ; 4383.0bp to feature; MODIFIER silent_mutation Average:43.694; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N
vg1012708940 C -> T LOC_Os10g24710.1 intron_variant ; MODIFIER silent_mutation Average:43.694; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N
vg1012708940 C -> DEL N N silent_mutation Average:43.694; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012708940 2.68E-09 4.46E-11 mr1210 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
vg1012708940 1.90E-08 1.68E-10 mr1305 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
vg1012708940 4.87E-10 2.74E-13 mr1585 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
vg1012708940 1.04E-08 1.56E-10 mr1586 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
vg1012708940 2.32E-06 2.32E-06 mr1649 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
vg1012708940 NA 6.13E-06 mr1765 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
vg1012708940 7.29E-10 6.04E-12 mr1305_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
vg1012708940 2.93E-06 5.81E-08 mr1409_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
vg1012708940 NA 7.17E-07 mr1559_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
vg1012708940 4.64E-09 6.45E-13 mr1585_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
vg1012708940 3.78E-06 4.16E-07 mr1703_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
vg1012708940 NA 7.87E-06 mr1765_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