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Detailed information for vg1118802157:

Variant ID: vg1118802157 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18802157
Reference Allele: CAlternative Allele: T,G
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GAATAAGTAAGGTGGTACTAAACTCCACATGCATGCCATCCCATGAGGTGGGCTTTTGTGATTTTTCAAAGAATTAATCTTCGAATAGGCCTTAGCCCAT[C/T,G]
TATTAATTCCAACAGTACTCTACAGAATTATTGATTTCTAAGGCATTATGTTGCAGAGGTTACCGACCGTACGTAGAAATAGTTTTCTTAGTTGTGTAAG

Reverse complement sequence

CTTACACAACTAAGAAAACTATTTCTACGTACGGTCGGTAACCTCTGCAACATAATGCCTTAGAAATCAATAATTCTGTAGAGTACTGTTGGAATTAATA[G/A,C]
ATGGGCTAAGGCCTATTCGAAGATTAATTCTTTGAAAAATCACAAAAGCCCACCTCATGGGATGGCATGCATGTGGAGTTTAGTACCACCTTACTTATTC

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 78.50% 21.00% 0.19% 0.00% G: 0.38%
All Indica  2759 64.70% 35.00% 0.29% 0.00% NA
All Japonica  1512 98.30% 0.50% 0.00% 0.00% G: 1.19%
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 46.10% 53.60% 0.34% 0.00% NA
Indica II  465 50.50% 48.40% 1.08% 0.00% NA
Indica III  913 76.00% 24.00% 0.00% 0.00% NA
Indica Intermediate  786 73.90% 26.00% 0.13% 0.00% NA
Temperate Japonica  767 97.00% 0.70% 0.00% 0.00% G: 2.35%
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg1118802157 C -> T LOC_Os11g31970.1 upstream_gene_variant ; 978.0bp to feature; MODIFIER silent_mutation Average:55.818; most accessible tissue: Minghui63 root, score: 69.344 N N N N
vg1118802157 C -> T LOC_Os11g31970-LOC_Os11g31980 intergenic_region ; MODIFIER silent_mutation Average:55.818; most accessible tissue: Minghui63 root, score: 69.344 N N N N
vg1118802157 C -> G LOC_Os11g31970.1 upstream_gene_variant ; 978.0bp to feature; MODIFIER silent_mutation Average:55.818; most accessible tissue: Minghui63 root, score: 69.344 N N N N
vg1118802157 C -> G LOC_Os11g31970-LOC_Os11g31980 intergenic_region ; MODIFIER silent_mutation Average:55.818; most accessible tissue: Minghui63 root, score: 69.344 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118802157 NA 2.45E-06 mr1312 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
vg1118802157 1.45E-07 3.80E-10 mr1377 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
vg1118802157 2.94E-06 2.94E-06 mr1377 Ind_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