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Detailed information for vg0421061649:

Variant ID: vg0421061649 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21061649
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CAACAATGCAACATGCGCATTATAGGCTTGAGAGGCATCTAGAGCTCTGTTTCAGCCACCTCATTATATTCTTGTTACCGTGATCCCTGAAGCAAGTGAC[C/G]
ACCAGATATCGACAATTCAACCCCAGTCCAGGGTTGTTTTCCGGTGTCTTTTGTGTACCACACCGTCACGTTCATGTGTTACCTCTCCTGCCTTAGTACT

Reverse complement sequence

AGTACTAAGGCAGGAGAGGTAACACATGAACGTGACGGTGTGGTACACAAAAGACACCGGAAAACAACCCTGGACTGGGGTTGAATTGTCGATATCTGGT[G/C]
GTCACTTGCTTCAGGGATCACGGTAACAAGAATATAATGAGGTGGCTGAAACAGAGCTCTAGATGCCTCTCAAGCCTATAATGCGCATGTTGCATTGTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.80%	11.90%	2.26%	0.00%	NA
All Indica	2759	97.60%	1.30%	1.05%	0.00%	NA
All Japonica	1512	66.50%	28.80%	4.70%	0.00%	NA
Aus	269	71.70%	26.80%	1.49%	0.00%	NA
Indica I	595	98.50%	0.00%	1.51%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	96.80%	1.40%	1.75%	0.00%	NA
Indica Intermediate	786	97.70%	1.90%	0.38%	0.00%	NA
Temperate Japonica	767	87.50%	6.80%	5.74%	0.00%	NA
Tropical Japonica	504	35.10%	61.90%	2.98%	0.00%	NA
Japonica Intermediate	241	65.60%	29.50%	4.98%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	21.10%	3.33%	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
vg0421061649	C -> G	LOC_Os04g34760.1	upstream_gene_variant ; 3020.0bp to feature; MODIFIER	silent_mutation	Average:48.453; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg0421061649	C -> G	LOC_Os04g34760-LOC_Os04g34780	intergenic_region ; MODIFIER	silent_mutation	Average:48.453; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421061649	NA	5.48E-08	mr1029	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
vg0421061649	NA	8.29E-11	mr1047	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
vg0421061649	NA	6.24E-08	mr1189	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
vg0421061649	NA	6.40E-07	mr1271	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
vg0421061649	NA	7.38E-06	mr1295	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
vg0421061649	NA	5.10E-08	mr1625	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
vg0421061649	NA	3.01E-08	mr1642	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
vg0421061649	NA	2.52E-06	mr1725	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
vg0421061649	NA	5.96E-07	mr1782	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
vg0421061649	NA	1.90E-07	mr1796	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
vg0421061649	4.65E-06	1.58E-09	mr1990	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
vg0421061649	NA	6.31E-12	mr1047_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
vg0421061649	NA	3.24E-12	mr1189_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
vg0421061649	NA	8.48E-10	mr1338_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
vg0421061649	NA	8.20E-09	mr1449_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
vg0421061649	NA	4.34E-09	mr1471_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
vg0421061649	NA	7.61E-10	mr1642_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
vg0421061649	NA	4.83E-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
vg0421061649	NA	2.56E-06	mr1815_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
vg0421061649	NA	1.44E-07	mr1819_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
vg0421061649	NA	1.25E-06	mr1966_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