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Detailed information for vg0630024751:

Variant ID: vg0630024751 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 30024751
Reference Allele: AAlternative Allele: G,AGATG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTAGCACCGCAACTTCCATTGGTGTTCGAGAGATAATTCTGCTCGCTCACTGGTTCTTGCACCAGTACGTAGCAATCTCTCGCACCGCAACTTCCATT[A/G,AGATG]
GTGTTCGAGAGATAATTCTGCTCGCTCACTGGTTCTCGCACCAATACGTAGCAATCTCTCGCACCTTAACTTCAGATGGTCGAGGTACGACTACGGCAGC

Reverse complement sequence

GCTGCCGTAGTCGTACCTCGACCATCTGAAGTTAAGGTGCGAGAGATTGCTACGTATTGGTGCGAGAACCAGTGAGCGAGCAGAATTATCTCTCGAACAC[T/C,CATCT]
AATGGAAGTTGCGGTGCGAGAGATTGCTACGTACTGGTGCAAGAACCAGTGAGCGAGCAGAATTATCTCTCGAACACCAATGGAAGTTGCGGTGCTAGAG

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 29.80% 0.20% 13.99% 56.03% NA
All Indica  2759 7.10% 0.20% 17.65% 75.03% NA
All Japonica  1512 73.70% 0.00% 0.93% 25.33% NA
Aus  269 3.30% 1.10% 55.39% 40.15% NA
Indica I  595 8.20% 0.00% 12.10% 79.66% NA
Indica II  465 1.30% 0.00% 11.18% 87.53% NA
Indica III  913 6.70% 0.10% 26.29% 66.92% NA
Indica Intermediate  786 10.20% 0.60% 15.65% 73.54% NA
Temperate Japonica  767 94.30% 0.00% 0.13% 5.61% NA
Tropical Japonica  504 40.70% 0.00% 2.38% 56.94% NA
Japonica Intermediate  241 77.60% 0.00% 0.41% 21.99% NA
VI/Aromatic  96 56.20% 0.00% 3.12% 40.62% NA
Intermediate  90 36.70% 1.10% 8.89% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630024751 A -> G LOC_Os06g49580.1 upstream_gene_variant ; 2387.0bp to feature; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> G LOC_Os06g49610.1 upstream_gene_variant ; 1961.0bp to feature; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> G LOC_Os06g49620.1 upstream_gene_variant ; 3969.0bp to feature; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> G LOC_Os06g49590.1 downstream_gene_variant ; 1360.0bp to feature; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> G LOC_Os06g49600.1 downstream_gene_variant ; 221.0bp to feature; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> G LOC_Os06g49600-LOC_Os06g49610 intergenic_region ; MODIFIER silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> DEL N N silent_mutation Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49580.1 upstream_gene_variant ; 2388.0bp to feature; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49610.1 upstream_gene_variant ; 1960.0bp to feature; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49620.1 upstream_gene_variant ; 3968.0bp to feature; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49590.1 downstream_gene_variant ; 1361.0bp to feature; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49600.1 downstream_gene_variant ; 222.0bp to feature; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0630024751 A -> AGATG LOC_Os06g49600-LOC_Os06g49610 intergenic_region ; MODIFIER N Average:15.423; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630024751 6.32E-07 NA mr1134_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
vg0630024751 NA 8.93E-06 mr1672_2 Ind_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