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Detailed information for vg0500831115:

Variant ID: vg0500831115 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 831115
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GCGAAATTCTATTGATAGAGCAGGAAAAAATTACAAGATTACAACCCTGGAGGGTCATAACCAGGAGAAAGAAAAAAATATACCACCACCCACACACCGG[C/T]
AGCGCCAACACACACGACCAGGAGAAGGTTAGCACCAGACCGGCCGCCGCTAGACCAACAAAGGAACACAGACGAGATCGCCCTACAGCAAGGGGGTGCC

Reverse complement sequence

GGCACCCCCTTGCTGTAGGGCGATCTCGTCTGTGTTCCTTTGTTGGTCTAGCGGCGGCCGGTCTGGTGCTAACCTTCTCCTGGTCGTGTGTGTTGGCGCT[G/A]
CCGGTGTGTGGGTGGTGGTATATTTTTTTCTTTCTCCTGGTTATGACCCTCCAGGGTTGTAATCTTGTAATTTTTTCCTGCTCTATCAATAGAATTTCGC

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 88.70% 11.20% 0.06% 0.00% NA
All Indica  2759 89.90% 10.10% 0.07% 0.00% NA
All Japonica  1512 91.60% 8.40% 0.00% 0.00% NA
Aus  269 74.00% 25.70% 0.37% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 85.10% 14.80% 0.11% 0.00% NA
Indica Intermediate  786 87.70% 12.20% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 79.00% 21.00% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 51.00% 49.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0500831115 C -> T LOC_Os05g02450.1 upstream_gene_variant ; 4479.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831115 C -> T LOC_Os05g02450.2 upstream_gene_variant ; 4479.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831115 C -> T LOC_Os05g02435.1 downstream_gene_variant ; 4975.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831115 C -> T LOC_Os05g02440.1 downstream_gene_variant ; 337.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831115 C -> T LOC_Os05g02435-LOC_Os05g02440 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500831115 NA 4.72E-07 mr1578_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
vg0500831115 2.28E-06 4.41E-07 mr1754_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
vg0500831115 NA 1.04E-07 mr1754_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
vg0500831115 5.94E-06 5.94E-06 mr1819_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
vg0500831115 NA 3.26E-06 mr1952_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