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Detailed information for vg1004874392:

Variant ID: vg1004874392 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4874392
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

ATACTAGCTAATACCCTCTATCCGATGCCCTCCTGGTACTTCGAGAAGCCACCCCTGACTGCCGAGTTCCTTACGATAGCCCGTCATGACCATACAACCG[G/A]
GGCTAAATACGGAGGAATACGCTCCTCAGGAAATTAACTTAGGATTATATATAGGCGCGGAGGAATACCCATACTGAGCTGTCACCATCAGCGGCCCACC

Reverse complement sequence

GGTGGGCCGCTGATGGTGACAGCTCAGTATGGGTATTCCTCCGCGCCTATATATAATCCTAAGTTAATTTCCTGAGGAGCGTATTCCTCCGTATTTAGCC[C/T]
CGGTTGTATGGTCATGACGGGCTATCGTAAGGAACTCGGCAGTCAGGGGTGGCTTCTCGAAGTACCAGGAGGGCATCGGATAGAGGGTATTAGCTAGTAT

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	76.10%	23.90%	0.04%	0.00%	NA
All Indica	2759	65.80%	34.10%	0.07%	0.00%	NA
All Japonica	1512	89.60%	10.40%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	69.10%	30.80%	0.17%	0.00%	NA
Indica II	465	62.40%	37.60%	0.00%	0.00%	NA
Indica III	913	62.50%	37.30%	0.11%	0.00%	NA
Indica Intermediate	786	69.10%	30.90%	0.00%	0.00%	NA
Temperate Japonica	767	94.50%	5.50%	0.00%	0.00%	NA
Tropical Japonica	504	81.50%	18.50%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	9.50%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg1004874392	G -> A	LOC_Os10g09000-LOC_Os10g09020	intergenic_region ; MODIFIER	silent_mutation	Average:41.163; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004874392	NA	6.16E-06	mr1709	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
vg1004874392	NA	3.52E-06	mr1053_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
vg1004874392	NA	3.39E-06	mr1128_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
vg1004874392	NA	8.45E-06	mr1147_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
vg1004874392	1.08E-06	1.08E-06	mr1151_2	Ind_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
vg1004874392	NA	9.43E-06	mr1204_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
vg1004874392	NA	7.34E-06	mr1220_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
vg1004874392	NA	3.46E-06	mr1250_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
vg1004874392	2.53E-06	2.53E-06	mr1250_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
vg1004874392	NA	1.46E-06	mr1691_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
vg1004874392	1.43E-06	9.50E-08	mr1705_2	Ind_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
vg1004874392	NA	8.21E-06	mr1729_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