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Detailed information for vg0421710470:

Variant ID: vg0421710470 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 21710470
Reference Allele: CAlternative Allele: G,CG
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.03, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTGCATTGCAACAAGATTTGCCTAACCGAACTGATCCATGGAAGCAAACCTGAAAAATGTATCAAGCTTAACCAATGTAAACAAAGAAAAAAATCAAA[C/G,CG]
GGGATGCTCATCACCTGGGATAACACCGGATAGAATATAACCTGCTCACGGCCATCAAGAAAGAATGTCGACGGCAGTGGCATGCATGCCAGGAGATACT

Reverse complement sequence

AGTATCTCCTGGCATGCATGCCACTGCCGTCGACATTCTTTCTTGATGGCCGTGAGCAGGTTATATTCTATCCGGTGTTATCCCAGGTGATGAGCATCCC[G/C,CG]
TTTGATTTTTTTCTTTGTTTACATTGGTTAAGCTTGATACATTTTTCAGGTTTGCTTCCATGGATCAGTTCGGTTAGGCAAATCTTGTTGCAATGCAGAG

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 73.70% 24.20% 1.02% 0.00% CG: 1.08%
All Indica  2759 91.10% 6.60% 0.58% 0.00% CG: 1.74%
All Japonica  1512 41.70% 56.30% 1.98% 0.00% NA
Aus  269 75.80% 22.70% 0.37% 0.00% CG: 1.12%
Indica I  595 94.60% 3.90% 1.18% 0.00% CG: 0.34%
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 87.00% 9.00% 0.00% 0.00% CG: 4.05%
Indica Intermediate  786 90.50% 7.30% 1.15% 0.00% CG: 1.15%
Temperate Japonica  767 41.60% 54.90% 3.52% 0.00% NA
Tropical Japonica  504 26.60% 73.00% 0.40% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.41% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 1.11% 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
vg0421710470 C -> CG LOC_Os04g35610.1 upstream_gene_variant ; 4814.0bp to feature; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0421710470 C -> CG LOC_Os04g35630.1 upstream_gene_variant ; 4350.0bp to feature; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0421710470 C -> CG LOC_Os04g35620.1 intron_variant ; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0421710470 C -> G LOC_Os04g35610.1 upstream_gene_variant ; 4813.0bp to feature; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0421710470 C -> G LOC_Os04g35630.1 upstream_gene_variant ; 4351.0bp to feature; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0421710470 C -> G LOC_Os04g35620.1 intron_variant ; MODIFIER silent_mutation Average:55.743; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421710470 NA 1.13E-06 mr1677 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
vg0421710470 NA 1.21E-06 mr1510_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
vg0421710470 NA 3.63E-06 mr1728_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
vg0421710470 1.32E-06 8.20E-09 mr1748_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
vg0421710470 NA 3.35E-08 mr1807_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