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Detailed information for vg0604641320:

Variant ID: vg0604641320 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4641320
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTAGCTGTGTGTTCAGTCGAATGTTTTTTTTAAAGGTTGTGTTAAATTGAAGGGTAGTTTTATCATTCTTAAGAAGGTACCTATAGGTACCATATTTT[C/T]
AAGTGTAAAATTTGATACCTCTAGATACTAAGTACTCTCCCCATCCCATAAAAATATAATCTAGTATTAGATGTGACACATCATAGTACTATGAATTTAA

Reverse complement sequence

TTAAATTCATAGTACTATGATGTGTCACATCTAATACTAGATTATATTTTTATGGGATGGGGAGAGTACTTAGTATCTAGAGGTATCAAATTTTACACTT[G/A]
AAAATATGGTACCTATAGGTACCTTCTTAAGAATGATAAAACTACCCTTCAATTTAACACAACCTTTAAAAAAAACATTCGACTGAACACACAGCTACTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.30% 43.70% 0.06% 0.00% NA
All Indica  2759 75.50% 24.50% 0.00% 0.00% NA
All Japonica  1512 17.30% 82.50% 0.20% 0.00% NA
Aus  269 70.60% 29.40% 0.00% 0.00% NA
Indica I  595 73.80% 26.20% 0.00% 0.00% NA
Indica II  465 60.40% 39.60% 0.00% 0.00% NA
Indica III  913 86.40% 13.60% 0.00% 0.00% NA
Indica Intermediate  786 73.00% 27.00% 0.00% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 31.30% 68.50% 0.20% 0.00% NA
Japonica Intermediate  241 33.60% 65.60% 0.83% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0604641320 C -> T LOC_Os06g09230.2 intron_variant ; MODIFIER silent_mutation Average:62.373; most accessible tissue: Callus, score: 82.687 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604641320 NA 2.04E-09 mr1141 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
vg0604641320 NA 3.87E-06 mr1695 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
vg0604641320 NA 5.52E-06 mr1755 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
vg0604641320 NA 3.25E-09 mr1141_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
vg0604641320 NA 2.49E-08 mr1695_2 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