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Detailed information for vg1114485005:

Variant ID: vg1114485005 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14485005
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGTAGCACCTTTGATACTCGGCTGAGCTGAGCCGTCTGGAGCTTGTTTTCCTTCTCCATCTTTAGAAGAACCGGTCCCAGGATCATCAGCAACCACTC[C/T]
TATCTTGTACTTTTGAACAAGTGTCCCCTTGCGGGTCTGCATAAATGAGTTCAAAAACTGATCCCGTGTTTGCTGCAACGTTGCTTCAAACTCTTTCTTC

Reverse complement sequence

GAAGAAAGAGTTTGAAGCAACGTTGCAGCAAACACGGGATCAGTTTTTGAACTCATTTATGCAGACCCGCAAGGGGACACTTGTTCAAAAGTACAAGATA[G/A]
GAGTGGTTGCTGATGATCCTGGGACCGGTTCTTCTAAAGATGGAGAAGGAAAACAAGCTCCAGACGGCTCAGCTCAGCCGAGTATCAAAGGTGCTACCGA

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 47.60% 34.90% 2.79% 14.73% NA
All Indica  2759 68.60% 2.50% 4.60% 24.32% NA
All Japonica  1512 3.20% 96.40% 0.07% 0.33% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.90% 4.90% 2.02% 21.18% NA
Indica II  465 50.50% 1.50% 9.03% 38.92% NA
Indica III  913 74.90% 0.40% 4.60% 20.04% NA
Indica Intermediate  786 69.30% 3.70% 3.94% 23.03% NA
Temperate Japonica  767 3.70% 96.10% 0.00% 0.26% NA
Tropical Japonica  504 3.00% 96.40% 0.20% 0.40% NA
Japonica Intermediate  241 2.10% 97.50% 0.00% 0.41% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 30.00% 43.30% 4.44% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1114485005 C -> T LOC_Os11g25400.1 missense_variant ; p.Gly78Arg; MODERATE nonsynonymous_codon ; G78R Average:26.64; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 benign -1.347 TOLERATED 0.05
vg1114485005 C -> DEL LOC_Os11g25400.1 N frameshift_variant Average:26.64; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114485005 NA 6.97E-08 mr1084_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
vg1114485005 4.17E-06 4.16E-06 mr1126_2 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
vg1114485005 NA 3.34E-07 mr1205_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
vg1114485005 NA 2.32E-07 mr1275_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
vg1114485005 NA 9.66E-24 mr1350_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
vg1114485005 NA 5.85E-15 mr1529_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
vg1114485005 NA 1.66E-06 mr1574_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
vg1114485005 NA 1.86E-14 mr1575_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
vg1114485005 NA 9.00E-06 mr1603_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
vg1114485005 NA 8.99E-17 mr1730_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
vg1114485005 NA 1.29E-17 mr1817_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
vg1114485005 NA 5.38E-10 mr1835_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
vg1114485005 NA 3.25E-15 mr1866_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
vg1114485005 NA 4.93E-06 mr1871_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
vg1114485005 NA 3.59E-14 mr1904_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
vg1114485005 7.29E-06 NA mr1938_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