Search for Variation information by Variation ID:

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

Detailed information for vg1005434645:

Variant ID: vg1005434645 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5434645
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGGGGTTTATTACTAATTGTTTCCACTTGTATTGGTAAATATATGCATGTAGGTGATTTTCAAAGAATTTACATCCTCCATGCAACGAAATATACCTC[C/T]
AGCCAATCATACGCGAGCACATGGATTGGAGGGCCCACATGATAGTCAAAATCGACCAGAAAGGGTCTTATCCACAGTGCATCGCCATAAGGCCCCACAT

Reverse complement sequence

ATGTGGGGCCTTATGGCGATGCACTGTGGATAAGACCCTTTCTGGTCGATTTTGACTATCATGTGGGCCCTCCAATCCATGTGCTCGCGTATGATTGGCT[G/A]
GAGGTATATTTCGTTGCATGGAGGATGTAAATTCTTTGAAAATCACCTACATGCATATATTTACCAATACAAGTGGAAACAATTAGTAATAAACCCCTAC

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 97.70% 1.60% 0.63% 0.00% NA
All Indica  2759 97.40% 1.50% 1.09% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 89.70% 5.70% 4.54% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1005434645 C -> T LOC_Os10g10010.1 upstream_gene_variant ; 4989.0bp to feature; MODIFIER silent_mutation Average:49.912; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N
vg1005434645 C -> T LOC_Os10g10020.1 upstream_gene_variant ; 1160.0bp to feature; MODIFIER silent_mutation Average:49.912; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N
vg1005434645 C -> T LOC_Os10g10010-LOC_Os10g10020 intergenic_region ; MODIFIER silent_mutation Average:49.912; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005434645 3.58E-06 1.44E-06 mr1177 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
vg1005434645 5.04E-06 2.98E-08 mr1053_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
vg1005434645 1.98E-06 8.25E-08 mr1128_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
vg1005434645 NA 2.04E-06 mr1147_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
vg1005434645 NA 5.96E-06 mr1264_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