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Detailed information for vg0702503501:

Variant ID: vg0702503501 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2503501
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCACAGTTTGATGGGGAGAACCCTAGAGCCTGGAAAATGAAGTGCGAAACCTATTTCCGTGTGAGTGGAATTTGCTCTGAAGTGTGGGTAGGTGTTGCT[T/G]
CTTTGCAATTTTCCGGGGGGGGGGGGGGGGGCTTTGACTTGGCTTCAATCCACAAATGCTCATGTTGAATTTATGGATTGGAGTGAGTTTTCTGAGCTAG

Reverse complement sequence

CTAGCTCAGAAAACTCACTCCAATCCATAAATTCAACATGAGCATTTGTGGATTGAAGCCAAGTCAAAGCCCCCCCCCCCCCCCCCGGAAAATTGCAAAG[A/C]
AGCAACACCTACCCACACTTCAGAGCAAATTCCACTCACACGGAAATAGGTTTCGCACTTCATTTTCCAGGCTCTAGGGTTCTCCCCATCAAACTGTGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.00% 37.00% 0.00% 0.00% NA
All Indica  2759 95.10% 4.90% 0.00% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 85.20% 14.80% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 28.10% 71.90% 0.00% 0.00% NA
Intermediate  90 47.80% 52.20% 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
vg0702503501 T -> G LOC_Os07g05440.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:50.215; most accessible tissue: Callus, score: 80.563 N N N N
vg0702503501 T -> G LOC_Os07g05440.1 5_prime_UTR_variant ; 2212.0bp to feature; MODIFIER silent_mutation Average:50.215; most accessible tissue: Callus, score: 80.563 N N N N
vg0702503501 T -> G LOC_Os07g05430.1 upstream_gene_variant ; 1830.0bp to feature; MODIFIER silent_mutation Average:50.215; most accessible tissue: Callus, score: 80.563 N N N N
vg0702503501 T -> G LOC_Os07g05440.2 intron_variant ; MODIFIER silent_mutation Average:50.215; most accessible tissue: Callus, score: 80.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702503501 NA 1.27E-07 mr1162 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
vg0702503501 NA 1.16E-11 mr1281 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
vg0702503501 NA 8.84E-38 mr1542 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
vg0702503501 NA 3.81E-11 mr1630 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
vg0702503501 NA 3.34E-08 mr1804 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
vg0702503501 NA 3.45E-20 mr1281_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