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Detailed information for vg1005803813:

Variant ID: vg1005803813 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5803813
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.22, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

AACAGCACTCCTTACAAAAATTTCGACTAAACTCGAAACCCTAACTCAAAACTTAACTCAATTGCTCTCTAAAGCGATACCGGGAAGCCTCACGCTCCCC[C/T]
CTCTATTTATACATGAGGTAGGCAGCCTAAAGCCCCGAACCAAACTCATACTAGGAGTCCTAAACACCTTAGGAAACCCACTAGTACAAGAAAGAAACTT

Reverse complement sequence

AAGTTTCTTTCTTGTACTAGTGGGTTTCCTAAGGTGTTTAGGACTCCTAGTATGAGTTTGGTTCGGGGCTTTAGGCTGCCTACCTCATGTATAAATAGAG[G/A]
GGGGAGCGTGAGGCTTCCCGGTATCGCTTTAGAGAGCAATTGAGTTAAGTTTTGAGTTAGGGTTTCGAGTTTAGTCGAAATTTTTGTAAGGAGTGCTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	21.10%	0.83%	0.00%	NA
All Indica	2759	73.20%	26.00%	0.76%	0.00%	NA
All Japonica	1512	98.60%	1.30%	0.13%	0.00%	NA
Aus	269	14.50%	83.30%	2.23%	0.00%	NA
Indica I	595	89.90%	9.40%	0.67%	0.00%	NA
Indica II	465	72.70%	26.70%	0.65%	0.00%	NA
Indica III	913	69.70%	30.00%	0.33%	0.00%	NA
Indica Intermediate	786	65.00%	33.60%	1.40%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	1.60%	0.20%	0.00%	NA
Japonica Intermediate	241	95.00%	4.60%	0.41%	0.00%	NA
VI/Aromatic	96	68.80%	22.90%	8.33%	0.00%	NA
Intermediate	90	82.20%	15.60%	2.22%	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
vg1005803813	C -> T	LOC_Os10g10520.1	upstream_gene_variant ; 812.0bp to feature; MODIFIER	silent_mutation	Average:38.99; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1005803813	C -> T	LOC_Os10g10520-LOC_Os10g10530	intergenic_region ; MODIFIER	silent_mutation	Average:38.99; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005803813	NA	1.90E-10	mr1027_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
vg1005803813	NA	1.25E-06	mr1057_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
vg1005803813	NA	5.77E-07	mr1252_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
vg1005803813	NA	4.34E-10	mr1580_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
vg1005803813	NA	6.27E-06	mr1662_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
vg1005803813	NA	2.83E-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
vg1005803813	NA	2.45E-11	mr1709_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
vg1005803813	NA	1.17E-07	mr1709_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
vg1005803813	NA	5.49E-09	mr1743_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
vg1005803813	NA	5.03E-06	mr1785_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
vg1005803813	NA	7.20E-06	mr1790_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
vg1005803813	2.24E-06	8.92E-11	mr1825_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
vg1005803813	NA	9.27E-06	mr1912_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
vg1005803813	NA	6.96E-06	mr1943_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
vg1005803813	NA	9.99E-06	mr1968_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