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Detailed information for vg1005678285:

Variant ID: vg1005678285 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5678285
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTGTCATATCCCGTACTAGTTTGTTTTTTATAGGACGGAGGGAGTAAATGATATGTCTCTAGACTGGCGTAGCGTATCCATTTGTTTTGCTGCAAGAG[C/T]
AATACAGTTGTTTAGGTATTGGGTTCTAAGCCGCACATAGGCTGGCTCTTGAACTCCTGTTAGAACTTTATTGGCAAATTTCAGGAGGAGAGCAGTGCGC

Reverse complement sequence

GCGCACTGCTCTCCTCCTGAAATTTGCCAATAAAGTTCTAACAGGAGTTCAAGAGCCAGCCTATGTGCGGCTTAGAACCCAATACCTAAACAACTGTATT[G/A]
CTCTTGCAGCAAAACAAATGGATACGCTACGCCAGTCTAGAGACATATCATTTACTCCCTCCGTCCTATAAAAAACAAACTAGTACGGGATATGACACAT

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 95.70% 3.40% 0.15% 0.66% NA
All Indica  2759 99.50% 0.50% 0.00% 0.07% NA
All Japonica  1512 92.50% 7.00% 0.13% 0.40% NA
Aus  269 98.50% 0.00% 0.00% 1.49% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.00% 0.90% 0.00% 0.11% NA
Indica Intermediate  786 99.40% 0.50% 0.00% 0.13% NA
Temperate Japonica  767 87.00% 12.90% 0.13% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.00% 0.40% NA
Japonica Intermediate  241 95.90% 2.10% 0.41% 1.66% NA
VI/Aromatic  96 39.60% 39.60% 4.17% 16.67% NA
Intermediate  90 88.90% 6.70% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005678285 C -> T LOC_Os10g10334.1 intron_variant ; MODIFIER silent_mutation Average:44.955; most accessible tissue: Callus, score: 70.863 N N N N
vg1005678285 C -> DEL N N silent_mutation Average:44.955; most accessible tissue: Callus, score: 70.863 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005678285 2.32E-10 NA mr1210 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
vg1005678285 8.86E-06 4.39E-09 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
vg1005678285 7.43E-11 NA mr1305 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
vg1005678285 5.82E-06 4.45E-09 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
vg1005678285 2.30E-06 3.43E-11 mr1585 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
vg1005678285 5.33E-06 6.49E-11 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
vg1005678285 1.58E-10 NA mr1586 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
vg1005678285 NA 4.22E-08 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
vg1005678285 4.45E-06 NA mr1649 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
vg1005678285 NA 7.03E-06 mr1765 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
vg1005678285 NA 1.42E-07 mr1915 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
vg1005678285 2.99E-08 NA mr1305_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
vg1005678285 1.33E-06 3.78E-09 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
vg1005678285 1.02E-06 2.09E-11 mr1585_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
vg1005678285 2.37E-07 9.29E-12 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