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Detailed information for vg1016341327:

Variant ID: vg1016341327 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16341327
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.07, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CATAATTCAGACTTTTTTCTCGTAGGAAAAAAAAACTATAACAACATGGGCATATATATCGTGTTGTCGTAGCAACTTACTCTCAACTAACCTAACCACA[A/G]
CACAACTGTATTATGATGTATTCTACAGAATAATGCCTTAAAAAAGGATAAATTTTATAGTTCTTAAGAAAGTTTGTGGAGGTGCCAAGATTTTACGCTA

Reverse complement sequence

TAGCGTAAAATCTTGGCACCTCCACAAACTTTCTTAAGAACTATAAAATTTATCCTTTTTTAAGGCATTATTCTGTAGAATACATCATAATACAGTTGTG[T/C]
TGTGGTTAGGTTAGTTGAGAGTAAGTTGCTACGACAACACGATATATATGCCCATGTTGTTATAGTTTTTTTTTCCTACGAGAAAAAAGTCTGAATTATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.30%	5.90%	1.99%	38.81%	NA
All Indica	2759	34.40%	0.40%	3.01%	62.20%	NA
All Japonica	1512	80.80%	15.00%	0.46%	3.70%	NA
Aus	269	82.90%	14.90%	0.00%	2.23%	NA
Indica I	595	33.80%	0.20%	4.54%	61.51%	NA
Indica II	465	25.60%	0.20%	2.58%	71.61%	NA
Indica III	913	37.80%	0.10%	2.96%	59.15%	NA
Indica Intermediate	786	36.30%	0.90%	2.16%	60.69%	NA
Temperate Japonica	767	87.20%	11.50%	0.39%	0.91%	NA
Tropical Japonica	504	89.50%	6.30%	0.00%	4.17%	NA
Japonica Intermediate	241	42.30%	44.40%	1.66%	11.62%	NA
VI/Aromatic	96	72.90%	0.00%	1.04%	26.04%	NA
Intermediate	90	57.80%	4.40%	3.33%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1016341327	A -> G	LOC_Os10g31180.1	upstream_gene_variant ; 581.0bp to feature; MODIFIER	silent_mutation	Average:24.213; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg1016341327	A -> G	LOC_Os10g31180-LOC_Os10g31189	intergenic_region ; MODIFIER	silent_mutation	Average:24.213; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg1016341327	A -> DEL	N	N	silent_mutation	Average:24.213; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016341327	8.36E-06	NA	mr1116	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
vg1016341327	7.47E-06	NA	mr1117	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
vg1016341327	2.02E-06	NA	mr1123	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
vg1016341327	5.20E-07	NA	mr1242	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
vg1016341327	1.63E-08	NA	mr1496	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
vg1016341327	NA	5.19E-06	mr1496	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
vg1016341327	1.52E-06	NA	mr1936	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
vg1016341327	6.44E-08	NA	mr1113_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
vg1016341327	NA	2.03E-06	mr1113_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
vg1016341327	5.38E-06	NA	mr1114_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
vg1016341327	2.92E-06	NA	mr1117_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
vg1016341327	7.26E-07	NA	mr1119_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
vg1016341327	6.52E-06	NA	mr1120_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
vg1016341327	3.21E-07	NA	mr1123_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
vg1016341327	3.52E-07	NA	mr1240_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
vg1016341327	NA	7.41E-06	mr1240_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
vg1016341327	1.07E-06	NA	mr1242_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
vg1016341327	4.15E-06	NA	mr1247_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
vg1016341327	8.35E-09	NA	mr1496_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
vg1016341327	NA	1.11E-06	mr1496_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