Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0718051702:

Variant ID: vg0718051702 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 18051702
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTAATCAAACGGCGGTGAGTAAGGTAGCTAGACATGTCCCACAATGTGACTTATCCATAGATGGTGATCGGCAACGAAGAAAACCAGAACAACGGGAA[C/T]
ACGACCAGCAACGGCATGGTCCCATAGAGAGAGAAACGGCAACGATGATCTCTTGTGGTGAACACAGCCGGGTGAGTACATCAAAACGTGTTCACGGACA

Reverse complement sequence

TGTCCGTGAACACGTTTTGATGTACTCACCCGGCTGTGTTCACCACAAGAGATCATCGTTGCCGTTTCTCTCTCTATGGGACCATGCCGTTGCTGGTCGT[G/A]
TTCCCGTTGTTCTGGTTTTCTTCGTTGCCGATCACCATCTATGGATAAGTCACATTGTGGGACATGTCTAGCTACCTTACTCACCGCCGTTTGATTACTG

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 49.50% 29.40% 9.54% 11.57% NA
All Indica  2759 44.20% 46.50% 2.28% 7.00% NA
All Japonica  1512 63.00% 0.70% 22.29% 14.02% NA
Aus  269 9.30% 27.10% 13.75% 49.81% NA
Indica I  595 83.00% 15.60% 0.17% 1.18% NA
Indica II  465 18.50% 77.60% 1.72% 2.15% NA
Indica III  913 31.50% 56.10% 3.83% 8.54% NA
Indica Intermediate  786 44.80% 40.30% 2.42% 12.47% NA
Temperate Japonica  767 66.90% 0.50% 22.03% 10.56% NA
Tropical Japonica  504 54.20% 0.80% 26.98% 18.06% NA
Japonica Intermediate  241 68.90% 1.20% 13.28% 16.60% NA
VI/Aromatic  96 88.50% 1.00% 8.33% 2.08% NA
Intermediate  90 63.30% 23.30% 6.67% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0718051702 C -> DEL N N silent_mutation Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N
vg0718051702 C -> T LOC_Os07g30510.1 upstream_gene_variant ; 592.0bp to feature; MODIFIER silent_mutation Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N
vg0718051702 C -> T LOC_Os07g30510-LOC_Os07g30530 intergenic_region ; MODIFIER silent_mutation Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0718051702 7.86E-07 2.71E-07 mr1211 Jap_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
vg0718051702 NA 6.20E-06 mr1184_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