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Detailed information for vg1118299752:

Variant ID: vg1118299752 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18299752
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCATGTCTCCCGAACAATTTCAGTACATATTGTGCAAGACGATTCTTGCATTAAATCAAAATTTGAAAAAGTGCCTCTACAGAGGTTAAAACGCCATAA[C/A]
AAAATTCCTTTACATATGAGGCAAATATTAAAGTGCAGAAAAGATGCCTCTACAACATTAATTTAACAAAATATGCTAAAAGTGCCTCTAAAAAGTATCT

Reverse complement sequence

AGATACTTTTTAGAGGCACTTTTAGCATATTTTGTTAAATTAATGTTGTAGAGGCATCTTTTCTGCACTTTAATATTTGCCTCATATGTAAAGGAATTTT[G/T]
TTATGGCGTTTTAACCTCTGTAGAGGCACTTTTTCAAATTTTGATTTAATGCAAGAATCGTCTTGCACAATATGTACTGAAATTGTTCGGGAGACATGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.70% 4.40% 0.91% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 84.10% 13.20% 2.65% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 0.00% NA
Temperate Japonica  767 73.10% 21.80% 5.08% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 88.00% 11.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg1118299752 C -> A LOC_Os11g31360.1 upstream_gene_variant ; 1574.0bp to feature; MODIFIER silent_mutation Average:35.589; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg1118299752 C -> A LOC_Os11g31340.1 downstream_gene_variant ; 2818.0bp to feature; MODIFIER silent_mutation Average:35.589; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg1118299752 C -> A LOC_Os11g31340-LOC_Os11g31360 intergenic_region ; MODIFIER silent_mutation Average:35.589; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118299752 1.86E-06 NA mr1031 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
vg1118299752 9.02E-06 7.80E-07 mr1031 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
vg1118299752 6.32E-06 NA mr1056 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
vg1118299752 NA 2.13E-06 mr1056 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