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Detailed information for vg0334633999:

Variant ID: vg0334633999 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34633999
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, A: 0.27, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCTCCTTTTCTAACTTCTGAAAATCACAAATGAACATGTCAGCATGCGACTCAGAAGCTCCACAACAACGTATTGCAAGATAAAGAGGGAAACCGCCT[C/A]
AAACTGTAGATAACAAGAAGCTGATACCATATAGTTCATTTCAAAACATATTTCAACCACACACCATGATTAATTGAAGCAGTGATATAAACCACAAAAT

Reverse complement sequence

ATTTTGTGGTTTATATCACTGCTTCAATTAATCATGGTGTGTGGTTGAAATATGTTTTGAAATGAACTATATGGTATCAGCTTCTTGTTATCTACAGTTT[G/T]
AGGCGGTTTCCCTCTTTATCTTGCAATACGTTGTTGTGGAGCTTCTGAGTCGCATGCTGACATGTTCATTTGTGATTTTCAGAAGTTAGAAAAGGAGAAA

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 51.10% 48.80% 0.08% 0.00% NA
All Indica  2759 23.90% 76.00% 0.14% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 49.80% 50.20% 0.00% 0.00% NA
Indica I  595 7.90% 91.80% 0.34% 0.00% NA
Indica II  465 21.90% 77.80% 0.22% 0.00% NA
Indica III  913 30.20% 69.80% 0.00% 0.00% NA
Indica Intermediate  786 29.80% 70.10% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 4.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0334633999 C -> A LOC_Os03g60950.1 3_prime_UTR_variant ; 740.0bp to feature; MODIFIER silent_mutation Average:58.05; most accessible tissue: Callus, score: 92.532 N N N N
vg0334633999 C -> A LOC_Os03g60960.1 upstream_gene_variant ; 2943.0bp to feature; MODIFIER silent_mutation Average:58.05; most accessible tissue: Callus, score: 92.532 N N N N
vg0334633999 C -> A LOC_Os03g60939.1 downstream_gene_variant ; 639.0bp to feature; MODIFIER silent_mutation Average:58.05; most accessible tissue: Callus, score: 92.532 N N N N
vg0334633999 C -> A LOC_Os03g60950.2 intron_variant ; MODIFIER silent_mutation Average:58.05; most accessible tissue: Callus, score: 92.532 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334633999 6.79E-10 7.31E-60 mr1671 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
vg0334633999 1.71E-09 8.86E-11 mr1671 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
vg0334633999 3.82E-15 1.08E-85 mr1671_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
vg0334633999 5.15E-16 2.90E-17 mr1671_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