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Detailed information for vg0906640167:

Variant ID: vg0906640167 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6640167
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GTACACCATAGTTAAAACTCTCTCACAATGTAAGTCATTCTAACATTTCCTATATTCATATTGATTTTAGTGAATCTAGATAGATATATATGTCTAGATT[C/T,A]
ATTAACATCAATATGAATGTGGAAAATGCTAGAATGACTTGCATTGTGAAACGGAGGGAGTATTAACTTTTGTCTGTCATAACACATGTGTAATTGATTA

Reverse complement sequence

TAATCAATTACACATGTGTTATGACAGACAAAAGTTAATACTCCCTCCGTTTCACAATGCAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAAT[G/A,T]
AATCTAGACATATATATCTATCTAGATTCACTAAAATCAATATGAATATAGGAAATGTTAGAATGACTTACATTGTGAGAGAGTTTTAACTATGGTGTAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.40% 24.80% 1.02% 0.72% A: 0.02%
All Indica  2759 60.10% 38.00% 0.58% 1.23% A: 0.04%
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 69.90% 19.00% 11.15% 0.00% NA
Indica I  595 65.90% 31.40% 1.01% 1.68% NA
Indica II  465 70.80% 28.40% 0.00% 0.86% NA
Indica III  913 46.50% 51.70% 0.33% 1.31% A: 0.11%
Indica Intermediate  786 65.30% 32.80% 0.89% 1.02% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 21.90% 2.08% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0906640167 C -> DEL N N silent_mutation Average:52.634; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N
vg0906640167 C -> T LOC_Os09g11850.1 downstream_gene_variant ; 2856.0bp to feature; MODIFIER silent_mutation Average:52.634; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N
vg0906640167 C -> T LOC_Os09g11840.1 intron_variant ; MODIFIER silent_mutation Average:52.634; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N
vg0906640167 C -> A LOC_Os09g11850.1 downstream_gene_variant ; 2856.0bp to feature; MODIFIER silent_mutation Average:52.634; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N
vg0906640167 C -> A LOC_Os09g11840.1 intron_variant ; MODIFIER silent_mutation Average:52.634; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906640167 NA 6.16E-06 mr1057 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
vg0906640167 1.20E-07 1.20E-07 mr1389 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
vg0906640167 2.05E-07 4.76E-09 mr1038_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
vg0906640167 NA 6.11E-07 mr1057_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
vg0906640167 1.12E-06 1.12E-06 mr1389_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