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Detailed information for vg0723469618:

Variant ID: vg0723469618 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23469618
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGTAGCCCTGTCAGAGGGCCCCATCGGCCTGGCCGGTCAGACCGCCATCGGCTCGGTCTGACCGACTACAGCTCGGTCGGCTCTGTATCGGCCATCCC[G/A]
AGCAGCATCGTCTCGGCCTCCAAGAGGCCGGTCTGACCGGGAAAGTGCCTCCGGTCAGACCGCCACTATGTAGCCGGTCTGACCGGCCAGGGCACGCCGA

Reverse complement sequence

TCGGCGTGCCCTGGCCGGTCAGACCGGCTACATAGTGGCGGTCTGACCGGAGGCACTTTCCCGGTCAGACCGGCCTCTTGGAGGCCGAGACGATGCTGCT[C/T]
GGGATGGCCGATACAGAGCCGACCGAGCTGTAGTCGGTCAGACCGAGCCGATGGCGGTCTGACCGGCCAGGCCGATGGGGCCCTCTGACAGGGCTACAAC

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 81.40% 16.30% 0.34% 2.01% NA
All Indica  2759 91.30% 7.60% 0.40% 0.72% NA
All Japonica  1512 62.00% 33.10% 0.33% 4.63% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 90.30% 5.40% 0.86% 3.44% NA
Indica III  913 87.60% 11.80% 0.55% 0.00% NA
Indica Intermediate  786 90.50% 8.80% 0.25% 0.51% NA
Temperate Japonica  767 86.80% 12.90% 0.26% 0.00% NA
Tropical Japonica  504 28.80% 59.90% 0.20% 11.11% NA
Japonica Intermediate  241 52.30% 41.10% 0.83% 5.81% NA
VI/Aromatic  96 64.60% 35.40% 0.00% 0.00% NA
Intermediate  90 67.80% 26.70% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0723469618 G -> DEL N N silent_mutation Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 N N N N
vg0723469618 G -> A LOC_Os07g39170.1 upstream_gene_variant ; 1076.0bp to feature; MODIFIER silent_mutation Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 N N N N
vg0723469618 G -> A LOC_Os07g39180.1 downstream_gene_variant ; 1710.0bp to feature; MODIFIER silent_mutation Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 N N N N
vg0723469618 G -> A LOC_Os07g39170-LOC_Os07g39180 intergenic_region ; MODIFIER silent_mutation Average:15.828; most accessible tissue: Minghui63 young leaf, score: 23.613 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723469618 4.16E-15 NA mr1563 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
vg0723469618 1.93E-12 2.59E-21 mr1563 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
vg0723469618 1.70E-18 NA mr1563_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
vg0723469618 8.33E-16 4.11E-25 mr1563_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