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Detailed information for vg0307374440:

Variant ID: vg0307374440 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7374440
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAAAACGTGTAATTAGCTCCTGGACACTTGGGGCCTTATTTTATTATTTCCTATGGATTTGGAGAGAGAAACACTTGTAAGAGTACGATTTTGCCCCT[G/A]
CCCTCACACCAGCCAGAACACCGCCGCCACCACCTCCGCCCTTGAGCCCCTTCCTTCCCCTTGCGCCAGCATGCTCCCAAGACACCCATAACTCTTTTTA

Reverse complement sequence

TAAAAAGAGTTATGGGTGTCTTGGGAGCATGCTGGCGCAAGGGGAAGGAAGGGGCTCAAGGGCGGAGGTGGTGGCGGCGGTGTTCTGGCTGGTGTGAGGG[C/T]
AGGGGCAAAATCGTACTCTTACAAGTGTTTCTCTCTCCAAATCCATAGGAAATAATAAAATAAGGCCCCAAGTGTCCAGGAGCTAATTACACGTTTTTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.60% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.90% 7.80% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 84.50% 15.00% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0307374440 G -> A LOC_Os03g13614.1 upstream_gene_variant ; 4798.0bp to feature; MODIFIER silent_mutation Average:50.249; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0307374440 G -> A LOC_Os03g13630.1 upstream_gene_variant ; 2570.0bp to feature; MODIFIER silent_mutation Average:50.249; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0307374440 G -> A LOC_Os03g13614.2 upstream_gene_variant ; 4798.0bp to feature; MODIFIER silent_mutation Average:50.249; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0307374440 G -> A LOC_Os03g13614.3 upstream_gene_variant ; 4798.0bp to feature; MODIFIER silent_mutation Average:50.249; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0307374440 G -> A LOC_Os03g13630-LOC_Os03g13640 intergenic_region ; MODIFIER silent_mutation Average:50.249; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307374440 NA 4.61E-06 mr1171 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
vg0307374440 NA 5.42E-06 mr1305 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
vg0307374440 NA 2.88E-06 mr1358 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
vg0307374440 6.37E-07 9.85E-06 mr1138_2 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
vg0307374440 NA 8.56E-06 mr1305_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
vg0307374440 NA 2.46E-06 mr1585_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