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Detailed information for vg1017647167:

Variant ID: vg1017647167 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17647167
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


AACATAAAGTGAGTTCAGCTAGCAATCATATAATAAAGATAAAGATAAATGACTAGGAGAACCAACCGTCAGGTTACTATCAATCTTGTCATCATTACAA[C/T]
GATTGACCAAACTTGCTGAAGTCAAGATGACAGTGCGCGTAGCTTTGCTTCCATGCCACTTTATAATCAAGCCTGTGCATGCAAAAAACCTCACGAAACC

Reverse complement sequence

GGTTTCGTGAGGTTTTTTGCATGCACAGGCTTGATTATAAAGTGGCATGGAAGCAAAGCTACGCGCACTGTCATCTTGACTTCAGCAAGTTTGGTCAATC[G/A]
TTGTAATGATGACAAGATTGATAGTAACCTGACGGTTGGTTCTCCTAGTCATTTATCTTTATCTTTATTATATGATTGCTAGCTGAACTCACTTTATGTT

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 93.70% 6.30% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 80.80% 19.10% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.00% 3.00% 0.00% 0.00% NA
Tropical Japonica  504 52.20% 47.60% 0.20% 0.00% NA
Japonica Intermediate  241 89.20% 10.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1017647167 C -> T LOC_Os10g33490.1 missense_variant ; p.Arg494His; MODERATE nonsynonymous_codon ; R494Y Average:44.336; most accessible tissue: Minghui63 root, score: 85.142 benign 1.451 TOLERATED 0.17
vg1017647167 C -> T LOC_Os10g33490.1 missense_variant ; p.Arg494His; MODERATE nonsynonymous_codon ; R494H Average:44.336; most accessible tissue: Minghui63 root, score: 85.142 benign 0.111 TOLERATED 0.37

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017647167 NA 4.93E-11 mr1248 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
vg1017647167 NA 1.79E-11 mr1248 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
vg1017647167 NA 1.45E-07 mr1338 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
vg1017647167 NA 4.81E-07 mr1425 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
vg1017647167 NA 8.39E-06 mr1425 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
vg1017647167 NA 1.66E-09 mr1769 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
vg1017647167 NA 7.53E-07 mr1951 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
vg1017647167 NA 1.61E-07 mr1039_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
vg1017647167 NA 9.21E-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
vg1017647167 NA 2.00E-09 mr1632_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
vg1017647167 NA 2.89E-08 mr1676_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
vg1017647167 NA 5.19E-07 mr1696_2 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
vg1017647167 NA 1.99E-08 mr1905_2 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