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Detailed information for vg1011018004:

Variant ID: vg1011018004 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11018004
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCCCTGAGCATAGTCCCGGTCCTCACCATTGACCAAGACTGACCTCAAGTCACCTGCACATAATCAGACAAAACAACCGTTTCTGGGCACAGATATCA[T/C]
AACCTGACCCACGTTAGTCACACGCACTCACACCAACATCCACACATAATTACAAACCAATTCATCGAATAAATCATTTTGCAAAGCCAATTGTTCATCA

Reverse complement sequence

TGATGAACAATTGGCTTTGCAAAATGATTTATTCGATGAATTGGTTTGTAATTATGTGTGGATGTTGGTGTGAGTGCGTGTGACTAACGTGGGTCAGGTT[A/G]
TGATATCTGTGCCCAGAAACGGTTGTTTTGTCTGATTATGTGCAGGTGACTTGAGGTCAGTCTTGGTCAATGGTGAGGACCGGGACTATGCTCAGGGAGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.70% 3.40% 13.12% 54.76% NA
All Indica  2759 14.40% 0.10% 16.46% 69.05% NA
All Japonica  1512 51.50% 10.10% 4.17% 34.26% NA
Aus  269 42.00% 0.00% 24.54% 33.46% NA
Indica I  595 12.10% 0.20% 15.63% 72.10% NA
Indica II  465 8.00% 0.00% 13.33% 78.71% NA
Indica III  913 19.30% 0.10% 19.50% 61.12% NA
Indica Intermediate  786 14.10% 0.30% 15.39% 70.23% NA
Temperate Japonica  767 70.40% 19.40% 1.43% 8.74% NA
Tropical Japonica  504 18.50% 0.40% 9.13% 72.02% NA
Japonica Intermediate  241 60.20% 0.80% 2.49% 36.51% NA
VI/Aromatic  96 35.40% 2.10% 22.92% 39.58% NA
Intermediate  90 37.80% 4.40% 16.67% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1011018004 T -> C LOC_Os10g21510.1 downstream_gene_variant ; 1122.0bp to feature; MODIFIER silent_mutation Average:12.873; most accessible tissue: Callus, score: 68.921 N N N N
vg1011018004 T -> C LOC_Os10g21510-LOC_Os10g21540 intergenic_region ; MODIFIER silent_mutation Average:12.873; most accessible tissue: Callus, score: 68.921 N N N N
vg1011018004 T -> DEL N N silent_mutation Average:12.873; most accessible tissue: Callus, score: 68.921 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011018004 NA 4.12E-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
vg1011018004 NA 1.23E-06 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
vg1011018004 NA 6.27E-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
vg1011018004 NA 1.83E-06 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
vg1011018004 9.00E-07 9.00E-07 mr1166_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
vg1011018004 NA 1.75E-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
vg1011018004 NA 1.59E-06 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
vg1011018004 1.43E-06 4.15E-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
vg1011018004 NA 1.69E-10 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
vg1011018004 NA 1.19E-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
vg1011018004 NA 2.38E-08 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