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Detailed information for vg1015945404:

Variant ID: vg1015945404 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15945404
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGGTACACTCCTCTCAGCCGGTCTATCAATTTTCCTTGGTGTTACAATAAATTCTGATAGATTTACCCCAGTCGGGCCGTAACGGATGTTTTCTGGGC[C/A]
ATGGTATACTTGAATTATATATTTGTTGGACATATCTGTCAACGAAATAACTAGATCATTCTTTTATGTAATAAACGCCTACAACGTAATATCTTATTAT

Reverse complement sequence

ATAATAAGATATTACGTTGTAGGCGTTTATTACATAAAAGAATGATCTAGTTATTTCGTTGACAGATATGTCCAACAAATATATAATTCAAGTATACCAT[G/T]
GCCCAGAAAACATCCGTTACGGCCCGACTGGGGTAAATCTATCAGAATTTATTGTAACACCAAGGAAAATTGATAGACCGGCTGAGAGGAGTGTACCTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.30% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 80.80% 19.20% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 90.70% 9.30% 0.00% 0.00% NA
Tropical Japonica  504 81.70% 18.30% 0.00% 0.00% NA
Japonica Intermediate  241 47.30% 52.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg1015945404 C -> A LOC_Os10g30620.1 upstream_gene_variant ; 2866.0bp to feature; MODIFIER silent_mutation Average:35.367; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg1015945404 C -> A LOC_Os10g30630.1 upstream_gene_variant ; 116.0bp to feature; MODIFIER silent_mutation Average:35.367; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg1015945404 C -> A LOC_Os10g30640.1 upstream_gene_variant ; 852.0bp to feature; MODIFIER silent_mutation Average:35.367; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg1015945404 C -> A LOC_Os10g30630-LOC_Os10g30640 intergenic_region ; MODIFIER silent_mutation Average:35.367; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015945404 1.13E-06 NA mr1534 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
vg1015945404 NA 2.13E-06 mr1534 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
vg1015945404 2.29E-09 NA mr1745 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
vg1015945404 NA 6.44E-07 mr1745 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
vg1015945404 6.02E-06 NA mr1745_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
vg1015945404 NA 5.40E-07 mr1745_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