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Detailed information for vg0203591903:

Variant ID: vg0203591903 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 3591903
Reference Allele: CAlternative Allele: A,CT
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAATATTTTTTTCTTTTTTTATCTCGTTTTCTTTTTCTTTTTTTTCCTTTGAGTTTTCCTTTTTTCTTCTCTCCCTCACTCTTTATTAATACGTTTTTT[C/A,CT]
TTTTTTTATCTCGTTTTCTTTTTCTATGTTTATTTATTTATTTTCTTTTTTTCTTGTAATACTATCTTCAAAATATATGTTTAATATGCAACTTTCTTTG

Reverse complement sequence

CAAAGAAAGTTGCATATTAAACATATATTTTGAAGATAGTATTACAAGAAAAAAAGAAAATAAATAAATAAACATAGAAAAAGAAAACGAGATAAAAAAA[G/T,AG]
AAAAAACGTATTAATAAAGAGTGAGGGAGAGAAGAAAAAAGGAAAACTCAAAGGAAAAAAAAGAAAAAGAAAACGAGATAAAAAAAGAAAAAAATATTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 1.00% 0.44% 2.45% CT: 0.06%
All Indica  2759 99.70% 0.00% 0.22% 0.00% CT: 0.07%
All Japonica  1512 88.40% 3.00% 0.99% 7.54% CT: 0.07%
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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.20% 0.00% 0.55% 0.00% CT: 0.22%
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 87.90% 0.70% 0.39% 11.08% NA
Tropical Japonica  504 91.30% 6.30% 2.18% 0.00% CT: 0.20%
Japonica Intermediate  241 84.20% 3.30% 0.41% 12.03% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 0.00% 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
vg0203591903 C -> A LOC_Os02g07020.1 upstream_gene_variant ; 3869.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> A LOC_Os02g07030.1 upstream_gene_variant ; 2406.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> A LOC_Os02g07030.2 upstream_gene_variant ; 2326.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> A LOC_Os02g07030.3 upstream_gene_variant ; 2327.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> A LOC_Os02g07020-LOC_Os02g07030 intergenic_region ; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> CT LOC_Os02g07020.1 upstream_gene_variant ; 3870.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> CT LOC_Os02g07030.1 upstream_gene_variant ; 2405.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> CT LOC_Os02g07030.2 upstream_gene_variant ; 2325.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> CT LOC_Os02g07030.3 upstream_gene_variant ; 2326.0bp to feature; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> CT LOC_Os02g07020-LOC_Os02g07030 intergenic_region ; MODIFIER silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0203591903 C -> DEL N N silent_mutation Average:22.854; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203591903 2.41E-06 2.41E-06 mr1591 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