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Detailed information for vg0307993242:

Variant ID: vg0307993242 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7993242
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCTCCATTGATTTGGGGCCGAGTTTTTCGCGTGCTAATAGTGAAGTACTGCAACGAGAGGGAGAGAGAGATGCAGAGGGGCAAAGGTGTAATTACACT[A/G]
CGTGCTATTGGTGTGGAGATGGCTGTGACCGTGAGCACAACGGTGAATTTCGCATGGGTGCATCAGGGCAATGCACGCTATTCACGCATCAAACCTAGTG

Reverse complement sequence

CACTAGGTTTGATGCGTGAATAGCGTGCATTGCCCTGATGCACCCATGCGAAATTCACCGTTGTGCTCACGGTCACAGCCATCTCCACACCAATAGCACG[T/C]
AGTGTAATTACACCTTTGCCCCTCTGCATCTCTCTCTCCCTCTCGTTGCAGTACTTCACTATTAGCACGCGAAAAACTCGGCCCCAAATCAATGGAGCGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 7.10% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 77.20% 21.50% 1.32% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 93.00% 5.70% 1.30% 0.00% NA
Tropical Japonica  504 73.60% 26.00% 0.40% 0.00% NA
Japonica Intermediate  241 34.40% 62.20% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0307993242 A -> G LOC_Os03g14710.1 upstream_gene_variant ; 4917.0bp to feature; MODIFIER silent_mutation Average:68.124; most accessible tissue: Callus, score: 97.897 N N N N
vg0307993242 A -> G LOC_Os03g14690.1 downstream_gene_variant ; 3805.0bp to feature; MODIFIER silent_mutation Average:68.124; most accessible tissue: Callus, score: 97.897 N N N N
vg0307993242 A -> G LOC_Os03g14700.1 intron_variant ; MODIFIER silent_mutation Average:68.124; most accessible tissue: Callus, score: 97.897 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307993242 NA 4.90E-13 mr1871 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
vg0307993242 1.86E-06 NA mr1238_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
vg0307993242 NA 4.65E-07 mr1308_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
vg0307993242 1.93E-06 NA mr1484_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
vg0307993242 NA 1.09E-07 mr1554_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
vg0307993242 8.69E-06 1.03E-08 mr1566_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
vg0307993242 NA 5.80E-07 mr1566_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
vg0307993242 NA 2.91E-07 mr1730_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
vg0307993242 NA 1.81E-07 mr1819_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
vg0307993242 NA 7.83E-06 mr1849_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
vg0307993242 NA 5.41E-06 mr1853_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
vg0307993242 NA 2.64E-06 mr1866_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
vg0307993242 NA 6.04E-12 mr1905_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
vg0307993242 NA 1.25E-06 mr1905_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