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Detailed information for vg0820151458:

Variant ID: vg0820151458 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20151458
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, A: 0.24, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGTCGCTGGCTACCCACCTTGCCATCGTACCGCGCTGCAACAGCCAGCGGGCTTCATCCACGACCACACGTCACCCGCGTACGAGATTAAGGGCACCA[A/C]
TGGTCATTCCTGTCACCACCCTCCTTGCTCACCGCACGGTTTTTCCAGTGGCGGCAGGATAGATGGTGGGAAGGAGGCCAGGCAACGCTGGATCTGCGGT

Reverse complement sequence

ACCGCAGATCCAGCGTTGCCTGGCCTCCTTCCCACCATCTATCCTGCCGCCACTGGAAAAACCGTGCGGTGAGCAAGGAGGGTGGTGACAGGAATGACCA[T/G]
TGGTGCCCTTAATCTCGTACGCGGGTGACGTGTGGTCGTGGATGAAGCCCGCTGGCTGTTGCAGCGCGGTACGATGGCAAGGTGGGTAGCCAGCGACAGC

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 35.10% 10.90% 0.32% 53.70% NA
All Indica  2759 22.50% 1.10% 0.25% 76.19% NA
All Japonica  1512 59.40% 30.90% 0.26% 9.46% NA
Aus  269 3.30% 0.70% 0.00% 95.91% NA
Indica I  595 3.70% 0.70% 0.17% 95.46% NA
Indica II  465 20.20% 1.50% 0.00% 78.28% NA
Indica III  913 31.30% 0.10% 0.44% 68.13% NA
Indica Intermediate  786 27.90% 2.20% 0.25% 69.72% NA
Temperate Japonica  767 45.80% 53.30% 0.13% 0.78% NA
Tropical Japonica  504 70.40% 5.40% 0.20% 24.01% NA
Japonica Intermediate  241 79.70% 12.90% 0.83% 6.64% NA
VI/Aromatic  96 90.60% 1.00% 1.04% 7.29% NA
Intermediate  90 50.00% 15.60% 3.33% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0820151458 A -> C LOC_Os08g32530.1 missense_variant ; p.Asn52Thr; MODERATE nonsynonymous_codon Average:48.224; most accessible tissue: Callus, score: 91.021 unknown unknown TOLERATED 0.06
vg0820151458 A -> DEL LOC_Os08g32530.1 N frameshift_variant Average:48.224; most accessible tissue: Callus, score: 91.021 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820151458 NA 9.15E-13 mr1182 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
vg0820151458 NA 1.02E-10 mr1282 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
vg0820151458 NA 1.12E-11 mr1650 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
vg0820151458 NA 7.80E-10 mr1658 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
vg0820151458 NA 1.12E-09 mr1712 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
vg0820151458 NA 4.18E-06 mr1910 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
vg0820151458 NA 1.14E-09 mr1002_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
vg0820151458 NA 2.57E-06 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
vg0820151458 NA 1.52E-17 mr1182_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
vg0820151458 NA 2.66E-08 mr1182_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
vg0820151458 NA 4.28E-08 mr1227_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
vg0820151458 NA 1.15E-13 mr1282_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
vg0820151458 NA 9.17E-07 mr1282_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
vg0820151458 NA 9.32E-08 mr1376_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
vg0820151458 NA 6.47E-08 mr1431_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
vg0820151458 NA 2.14E-08 mr1551_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
vg0820151458 NA 1.62E-07 mr1606_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
vg0820151458 NA 1.89E-07 mr1607_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
vg0820151458 NA 3.72E-11 mr1667_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
vg0820151458 2.93E-06 NA mr1670_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
vg0820151458 NA 6.22E-09 mr1681_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
vg0820151458 NA 2.08E-06 mr1730_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
vg0820151458 NA 1.79E-18 mr1980_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
vg0820151458 NA 3.20E-06 mr1980_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