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Detailed information for vg1122492947:

Variant ID: vg1122492947 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22492947
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAATTTGGTGGTTCTAAAATTTTACACTGGAAATTTTGTTACGTACTTAGTATCTATAGGTATCAAAATTTACATTAGAAAATATAATACCTCCCAGTAT[C/T]
TTCTCAAGGATGGTAAAATTATCCTTAATATTATTCTCCAATTTTTCATGGACTGTTCACCTTTCGTGCGATCGAGTCAGATAAGCTGTATCTTTTATTA

Reverse complement sequence

TAATAAAAGATACAGCTTATCTGACTCGATCGCACGAAAGGTGAACAGTCCATGAAAAATTGGAGAATAATATTAAGGATAATTTTACCATCCTTGAGAA[G/A]
ATACTGGGAGGTATTATATTTTCTAATGTAAATTTTGATACCTATAGATACTAAGTACGTAACAAAATTTCCAGTGTAAAATTTTAGAACCACCAAATTC

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 87.40% 12.50% 0.04% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 61.60% 38.30% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 54.20% 45.60% 0.13% 0.00% NA
Tropical Japonica  504 74.60% 25.20% 0.20% 0.00% NA
Japonica Intermediate  241 57.70% 42.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 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
vg1122492947 C -> T LOC_Os11g37920.1 3_prime_UTR_variant ; 198.0bp to feature; MODIFIER silent_mutation Average:71.946; most accessible tissue: Zhenshan97 flower, score: 89.315 N N N N
vg1122492947 C -> T LOC_Os11g37910.1 downstream_gene_variant ; 2334.0bp to feature; MODIFIER silent_mutation Average:71.946; most accessible tissue: Zhenshan97 flower, score: 89.315 N N N N
vg1122492947 C -> T LOC_Os11g37930.1 downstream_gene_variant ; 2119.0bp to feature; MODIFIER silent_mutation Average:71.946; most accessible tissue: Zhenshan97 flower, score: 89.315 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122492947 8.66E-07 NA mr1238 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
vg1122492947 5.72E-06 NA mr1309 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
vg1122492947 2.97E-09 NA mr1238_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
vg1122492947 1.92E-09 NA mr1484_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
vg1122492947 1.12E-08 NA mr1841_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
vg1122492947 1.54E-08 6.64E-20 mr1900_2 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
vg1122492947 5.34E-07 NA mr1945_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