Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0820151458:

Variant ID: vg0820151458 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20151458
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary 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 Size	Frequency 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