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Detailed information for vg0922498959:

Variant ID: vg0922498959 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 22498959
Reference Allele: GAlternative Allele: C,GGC
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAACTTTGCGCTGAACTAAACACAGTCTAAGGATAGGTATCTCTTGCGGATAGATTTCAAAACCTATGGACGATATGGTAATATAGATCTCTAAACTGTT[G/C,GGC]
TTACAAAGTTGCTCTTGGTTGTACCTGCTTTTAATTGAGTACGGTACGGTATATATGTTGGGTTCGCATTATTTGGTCGCCATTTAATTTGCAGTCAAAA

Reverse complement sequence

TTTTGACTGCAAATTAAATGGCGACCAAATAATGCGAACCCAACATATATACCGTACCGTACTCAATTAAAAGCAGGTACAACCAAGAGCAACTTTGTAA[C/G,GCC]
AACAGTTTAGAGATCTATATTACCATATCGTCCATAGGTTTTGAAATCTATCCGCAAGAGATACCTATCCTTAGACTGTGTTTAGTTCAGCGCAAAGTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.30% 36.60% 0.04% 0.00% GGC: 0.06%
All Indica  2759 40.30% 59.60% 0.07% 0.00% GGC: 0.11%
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 78.10% 21.90% 0.00% 0.00% NA
Indica I  595 33.60% 66.40% 0.00% 0.00% NA
Indica II  465 26.50% 73.10% 0.00% 0.00% GGC: 0.43%
Indica III  913 49.60% 50.10% 0.22% 0.00% GGC: 0.11%
Indica Intermediate  786 42.60% 57.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0922498959 G -> C LOC_Os09g39170.1 upstream_gene_variant ; 4639.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922498959 G -> C LOC_Os09g39170-LOC_Os09g39180 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922498959 G -> GGC LOC_Os09g39170.1 upstream_gene_variant ; 4640.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922498959 G -> GGC LOC_Os09g39170-LOC_Os09g39180 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922498959 3.01E-19 NA mr1865 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
vg0922498959 1.38E-18 3.94E-21 mr1865 Ind_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
vg0922498959 NA 1.88E-07 mr1045_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
vg0922498959 4.99E-18 NA mr1865_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
vg0922498959 3.04E-17 8.32E-22 mr1865_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
vg0922498959 NA 3.14E-07 mr1925_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