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Detailed information for vg0529371849:

Variant ID: vg0529371849 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29371849
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CTGGCGAGCGGGATGGAGTAGCCCACGAGCGACGGCGCAGCACAGAGGAGGAGGCAAACCCTAGATTGATTTCGTGTGTTTTGCGTGAAGGCGGCGGCTC[A/G]
GTTTATATAGGATAGGTCACTTGATCAGGGCGCCCGCACGATCTCCAGTCCGCGTAACCGAACCGGATAAGTCGCGCGTAACTTATCCGGACTCCATGCC

Reverse complement sequence

GGCATGGAGTCCGGATAAGTTACGCGCGACTTATCCGGTTCGGTTACGCGGACTGGAGATCGTGCGGGCGCCCTGATCAAGTGACCTATCCTATATAAAC[T/C]
GAGCCGCCGCCTTCACGCAAAACACACGAAATCAATCTAGGGTTTGCCTCCTCCTCTGTGCTGCGCCGTCGCTCGTGGGCTACTCCATCCCGCTCGCCAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.10%	35.80%	0.15%	0.00%	NA
All Indica	2759	95.10%	4.70%	0.25%	0.00%	NA
All Japonica	1512	4.80%	95.20%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	98.20%	1.30%	0.50%	0.00%	NA
Indica II	465	83.90%	15.70%	0.43%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	94.80%	5.00%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	13.10%	86.90%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	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
vg0529371849	A -> G	LOC_Os05g51200.1	upstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:47.85; most accessible tissue: Minghui63 root, score: 65.927	N	N	N	N
vg0529371849	A -> G	LOC_Os05g51200-LOC_Os05g51210	intergenic_region ; MODIFIER	silent_mutation	Average:47.85; most accessible tissue: Minghui63 root, score: 65.927	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529371849	NA	5.96E-15	mr1146	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
vg0529371849	NA	1.24E-08	mr1275	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
vg0529371849	NA	4.82E-21	mr1588	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
vg0529371849	NA	2.44E-18	mr1162_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
vg0529371849	NA	4.61E-16	mr1342_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
vg0529371849	NA	5.68E-10	mr1349_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
vg0529371849	NA	1.80E-06	mr1349_2	Ind_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
vg0529371849	NA	8.54E-29	mr1588_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
vg0529371849	NA	1.50E-07	mr1588_2	Ind_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
vg0529371849	NA	3.77E-07	mr1654_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
vg0529371849	NA	3.09E-17	mr1712_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
vg0529371849	NA	1.84E-12	mr1722_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
vg0529371849	NA	6.47E-08	mr1749_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
vg0529371849	NA	1.79E-07	mr1821_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