Search for Variation information by Variation ID:

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

Detailed information for vg1000239130:

Variant ID: vg1000239130 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 239130
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCTTCAACACCGAAAATGATATGGAAGACACTTCAAAAGTTCATAGGTACAAGTATAGCTTGGAATACTTTCTATGTTTGCATCATTATACATGAAGC[C/T]
TTTGCTCTATTGAATTCAATGAGCTTTACTCAGGGACAAGTAAAGGATAAGTGTTGCGGTGTTGTTGACGGTCGTTAAGTGCAAACTTTAACCGAACTCC

Reverse complement sequence

GGAGTTCGGTTAAAGTTTGCACTTAACGACCGTCAACAACACCGCAACACTTATCCTTTACTTGTCCCTGAGTAAAGCTCATTGAATTCAATAGAGCAAA[G/A]
GCTTCATGTATAATGATGCAAACATAGAAAGTATTCCAAGCTATACTTGTACCTATGAACTTTTGAAGTGTCTTCCATATCATTTTCGGTGTTGAAGAAT

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 36.90% 1.00% 34.93% 27.15% NA
All Indica  2759 30.00% 1.50% 51.65% 16.85% NA
All Japonica  1512 55.70% 0.30% 5.95% 38.10% NA
Aus  269 8.90% 0.70% 35.69% 54.65% NA
Indica I  595 20.30% 1.70% 63.19% 14.79% NA
Indica II  465 47.50% 0.60% 38.28% 13.55% NA
Indica III  913 23.70% 2.10% 53.34% 20.92% NA
Indica Intermediate  786 34.40% 1.10% 48.85% 15.65% NA
Temperate Japonica  767 85.80% 0.00% 1.30% 12.91% NA
Tropical Japonica  504 11.70% 0.80% 12.90% 74.60% NA
Japonica Intermediate  241 51.90% 0.00% 6.22% 41.91% NA
VI/Aromatic  96 11.50% 0.00% 21.88% 66.67% NA
Intermediate  90 44.40% 0.00% 21.11% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000239130 C -> T LOC_Os10g01400.1 upstream_gene_variant ; 4408.0bp to feature; MODIFIER silent_mutation Average:8.735; most accessible tissue: Zhenshan97 flower, score: 17.42 N N N N
vg1000239130 C -> T LOC_Os10g01390.1 downstream_gene_variant ; 26.0bp to feature; MODIFIER silent_mutation Average:8.735; most accessible tissue: Zhenshan97 flower, score: 17.42 N N N N
vg1000239130 C -> T LOC_Os10g01380-LOC_Os10g01390 intergenic_region ; MODIFIER silent_mutation Average:8.735; most accessible tissue: Zhenshan97 flower, score: 17.42 N N N N
vg1000239130 C -> DEL N N silent_mutation Average:8.735; most accessible tissue: Zhenshan97 flower, score: 17.42 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000239130 1.16E-06 1.16E-06 mr1260 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
vg1000239130 NA 6.02E-06 mr1300 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
vg1000239130 NA 2.41E-06 mr1570 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
vg1000239130 NA 2.04E-07 mr1310_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
vg1000239130 NA 3.46E-08 mr1959_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