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Detailed information for vg1011003709:

Variant ID: vg1011003709 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11003709
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


GGCAACGGCCGGCGCGAGGCGGGCACTGGAGTGTCCACCACCCCCTCCCACTCCGCCTCGCCACCTCCATGTCGTCGTCGTCGTCGTCTGCATGTCCTTC[C/A]
CCCTCTCCCGTTGCTCCAGCCTCCATCTCCGTCTCCTCCGCCATCGAATTCCACACGCTCTACTACCACATCAAGGTGACGCGCACACCCTCTACGTGTA

Reverse complement sequence

TACACGTAGAGGGTGTGCGCGTCACCTTGATGTGGTAGTAGAGCGTGTGGAATTCGATGGCGGAGGAGACGGAGATGGAGGCTGGAGCAACGGGAGAGGG[G/T]
GAAGGACATGCAGACGACGACGACGACGACATGGAGGTGGCGAGGCGGAGTGGGAGGGGGTGGTGGACACTCCAGTGCCCGCCTCGCGCCGGCCGTTGCC

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 89.90% 6.20% 0.47% 3.45% NA
All Indica  2759 90.40% 3.20% 0.76% 5.65% NA
All Japonica  1512 86.40% 13.30% 0.07% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.00% 0.70% 0.00% 0.34% NA
Indica II  465 92.50% 0.00% 1.72% 5.81% NA
Indica III  913 87.20% 4.80% 0.66% 7.34% NA
Indica Intermediate  786 86.50% 5.00% 0.89% 7.63% NA
Temperate Japonica  767 81.60% 18.30% 0.13% 0.00% NA
Tropical Japonica  504 96.40% 3.20% 0.00% 0.40% NA
Japonica Intermediate  241 80.90% 18.70% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 5.60% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1011003709 C -> A LOC_Os10g21479.1 upstream_gene_variant ; 197.0bp to feature; MODIFIER silent_mutation Average:79.007; most accessible tissue: Zhenshan97 young leaf, score: 92.871 N N N N
vg1011003709 C -> A LOC_Os10g21490.1 downstream_gene_variant ; 3547.0bp to feature; MODIFIER silent_mutation Average:79.007; most accessible tissue: Zhenshan97 young leaf, score: 92.871 N N N N
vg1011003709 C -> A LOC_Os10g21479-LOC_Os10g21490 intergenic_region ; MODIFIER silent_mutation Average:79.007; most accessible tissue: Zhenshan97 young leaf, score: 92.871 N N N N
vg1011003709 C -> DEL N N silent_mutation Average:79.007; most accessible tissue: Zhenshan97 young leaf, score: 92.871 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011003709 NA 1.56E-06 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
vg1011003709 NA 3.23E-07 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
vg1011003709 NA 4.02E-08 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
vg1011003709 NA 6.35E-07 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
vg1011003709 3.42E-06 3.42E-06 mr1166_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
vg1011003709 3.86E-06 NA mr1305_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
vg1011003709 NA 2.43E-08 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
vg1011003709 NA 8.19E-07 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
vg1011003709 2.07E-06 1.63E-06 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
vg1011003709 8.88E-09 1.72E-07 mr1585_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
vg1011003709 4.70E-07 3.02E-12 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
vg1011003709 NA 4.45E-06 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
vg1011003709 5.42E-08 NA mr1765_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
vg1011003709 1.88E-08 2.32E-11 mr1765_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