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Detailed information for vg0316049074:

Variant ID: vg0316049074 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16049074
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCTCCTATCTCTTCTCATCTCTCTCTATATTCTCTCTCAGAGGCGTGCTCACACGGGGAGGCATCGGTCGCGGCGGAGATGGCGAGGACGGCGGCCAG[C/T]
GGAGTGAAGCGGGGCAGCAGCGGCGGTGGACGAGCGCACGGCCGGCGGAGCGGCATCATCGGCCGAGCAGAGTGGCAGCAGTGGCGAGCGAGCGCGCGGC

Reverse complement sequence

GCCGCGCGCTCGCTCGCCACTGCTGCCACTCTGCTCGGCCGATGATGCCGCTCCGCCGGCCGTGCGCTCGTCCACCGCCGCTGCTGCCCCGCTTCACTCC[G/A]
CTGGCCGCCGTCCTCGCCATCTCCGCCGCGACCGATGCCTCCCCGTGTGAGCACGCCTCTGAGAGAGAATATAGAGAGAGATGAGAAGAGATAGGAGATA

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 89.20% 10.40% 0.42% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 70.60% 28.20% 1.19% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 70.30% 27.80% 1.96% 0.00% NA
Tropical Japonica  504 69.80% 29.80% 0.40% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.41% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 2.22% 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
vg0316049074 C -> T LOC_Os03g27940.1 missense_variant ; p.Arg43Trp; MODERATE nonsynonymous_codon ; R43W Average:75.717; most accessible tissue: Zhenshan97 young leaf, score: 86.542 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316049074 6.02E-06 NA mr1087_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
vg0316049074 NA 2.37E-06 mr1329_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
vg0316049074 NA 8.47E-07 mr1524_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
vg0316049074 8.40E-06 NA mr1549_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
vg0316049074 2.09E-07 NA mr1757_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
vg0316049074 NA 9.37E-06 mr1757_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
vg0316049074 3.40E-06 NA mr1980_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