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Detailed information for vg0319082408:

Variant ID: vg0319082408 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19082408
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACCCTAGTGATCGAGGCTTGGGTAGTCCTCTCCATGGGCCGGCTCCCGCCTTGCCCACCCCTTGACGAAGGGGGCGTGCGGTGGCTTCGAGGTTGAGCA[C/G]
TGGAGTTGGGATCGCCTCAACGGGGAGTAGGAAACCGGCAAGTTGCCGAACCTCGGTGAAAAATCTCTTGTCTCCTTGTCTCATTTACTTGTTGCATTTA

Reverse complement sequence

TAAATGCAACAAGTAAATGAGACAAGGAGACAAGAGATTTTTCACCGAGGTTCGGCAACTTGCCGGTTTCCTACTCCCCGTTGAGGCGATCCCAACTCCA[G/C]
TGCTCAACCTCGAAGCCACCGCACGCCCCCTTCGTCAAGGGGTGGGCAAGGCGGGAGCCGGCCCATGGAGAGGACTACCCAAGCCTCGATCACTAGGGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.00% 32.50% 0.25% 14.22% NA
All Indica  2759 78.50% 3.30% 0.22% 17.98% NA
All Japonica  1512 2.00% 86.60% 0.26% 11.18% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 92.90% 3.00% 0.00% 4.03% NA
Indica II  465 74.40% 3.20% 0.43% 21.94% NA
Indica III  913 69.40% 1.40% 0.11% 29.03% NA
Indica Intermediate  786 80.50% 5.70% 0.38% 13.36% NA
Temperate Japonica  767 0.30% 99.60% 0.13% 0.00% NA
Tropical Japonica  504 5.00% 66.30% 0.40% 28.37% NA
Japonica Intermediate  241 1.20% 87.60% 0.41% 10.79% NA
VI/Aromatic  96 25.00% 72.90% 0.00% 2.08% NA
Intermediate  90 45.60% 46.70% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0319082408 C -> DEL N N silent_mutation Average:34.415; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0319082408 C -> G LOC_Os03g33380.1 upstream_gene_variant ; 1954.0bp to feature; MODIFIER silent_mutation Average:34.415; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0319082408 C -> G LOC_Os03g33370.1 downstream_gene_variant ; 1800.0bp to feature; MODIFIER silent_mutation Average:34.415; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0319082408 C -> G LOC_Os03g33370-LOC_Os03g33380 intergenic_region ; MODIFIER silent_mutation Average:34.415; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319082408 NA 2.52E-06 mr1125 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
vg0319082408 NA 2.39E-10 mr1136 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
vg0319082408 NA 1.78E-10 mr1188 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
vg0319082408 NA 3.67E-08 mr1188 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
vg0319082408 NA 8.55E-11 mr1281 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
vg0319082408 NA 9.70E-06 mr1334 Ind_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
vg0319082408 4.31E-08 5.14E-10 mr1448 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
vg0319082408 NA 2.57E-20 mr1588 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
vg0319082408 NA 4.45E-08 mr1718 Ind_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
vg0319082408 6.33E-07 2.80E-117 mr1750 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
vg0319082408 5.89E-11 2.94E-20 mr1750 Ind_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
vg0319082408 NA 2.04E-11 mr1902 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
vg0319082408 4.10E-06 4.10E-06 mr1987 Ind_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
vg0319082408 NA 5.29E-08 mr1125_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
vg0319082408 2.97E-06 6.86E-12 mr1188_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
vg0319082408 NA 4.73E-10 mr1718_2 Ind_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
vg0319082408 NA 4.17E-11 mr1722_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
vg0319082408 1.91E-07 1.50E-20 mr1750_2 Ind_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
vg0319082408 NA 1.41E-13 mr1827_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
vg0319082408 NA 1.92E-10 mr1893_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