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Detailed information for vg1004685372:

Variant ID: vg1004685372 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4685372
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTTGAGAAGTGCTCATCTCTCCCGGTTCGCAACCCCCTTTACTCCCGGGTAGCGAATCGGGAGGGAGAATCCGGGACTAAAGATGACGGTCTTTAGTC[C/T]
CGGTTCAAATACCCAGGAGTAAATCTCCATCTTTAGTCCCGGTTGGTGACACCAACCGGGACTAAAGATGGCTGAGCCACGTGACCGGCAAAGCCATAAC

Reverse complement sequence

GTTATGGCTTTGCCGGTCACGTGGCTCAGCCATCTTTAGTCCCGGTTGGTGTCACCAACCGGGACTAAAGATGGAGATTTACTCCTGGGTATTTGAACCG[G/A]
GACTAAAGACCGTCATCTTTAGTCCCGGATTCTCCCTCCCGATTCGCTACCCGGGAGTAAAGGGGGTTGCGAACCGGGAGAGATGAGCACTTCTCAAGTA

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 94.30% 3.10% 0.02% 2.60% NA
All Indica  2759 96.40% 0.00% 0.00% 3.55% NA
All Japonica  1512 90.30% 9.50% 0.00% 0.20% 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 99.10% 0.00% 0.00% 0.86% NA
Indica III  913 91.80% 0.00% 0.00% 8.21% NA
Indica Intermediate  786 97.50% 0.10% 0.00% 2.42% NA
Temperate Japonica  767 89.70% 10.30% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 76.30% 22.40% 0.00% 1.24% NA
VI/Aromatic  96 78.10% 1.00% 0.00% 20.83% NA
Intermediate  90 94.40% 2.20% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004685372 C -> T LOC_Os10g08630.1 upstream_gene_variant ; 83.0bp to feature; MODIFIER silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N
vg1004685372 C -> T LOC_Os10g08640.1 upstream_gene_variant ; 288.0bp to feature; MODIFIER silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N
vg1004685372 C -> T LOC_Os10g08620.1 downstream_gene_variant ; 2478.0bp to feature; MODIFIER silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N
vg1004685372 C -> T LOC_Os10g08650.1 downstream_gene_variant ; 2598.0bp to feature; MODIFIER silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N
vg1004685372 C -> T LOC_Os10g08630-LOC_Os10g08640 intergenic_region ; MODIFIER silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N
vg1004685372 C -> DEL N N silent_mutation Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004685372 3.32E-06 3.32E-06 mr1647_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