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Detailed information for vg1005803839:

Variant ID: vg1005803839 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5803839
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.23, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CTAAACTCGAAACCCTAACTCAAAACTTAACTCAATTGCTCTCTAAAGCGATACCGGGAAGCCTCACGCTCCCCCCTCTATTTATACATGAGGTAGGCAG[C/T]
CTAAAGCCCCGAACCAAACTCATACTAGGAGTCCTAAACACCTTAGGAAACCCACTAGTACAAGAAAGAAACTTTACATAACCAAACGTACCAAATTTGG

Reverse complement sequence

CCAAATTTGGTACGTTTGGTTATGTAAAGTTTCTTTCTTGTACTAGTGGGTTTCCTAAGGTGTTTAGGACTCCTAGTATGAGTTTGGTTCGGGGCTTTAG[G/A]
CTGCCTACCTCATGTATAAATAGAGGGGGGAGCGTGAGGCTTCCCGGTATCGCTTTAGAGAGCAATTGAGTTAAGTTTTGAGTTAGGGTTTCGAGTTTAG

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	77.00%	21.20%	1.84%	0.00%	NA
All Indica	2759	72.40%	26.30%	1.34%	0.00%	NA
All Japonica	1512	98.70%	1.20%	0.13%	0.00%	NA
Aus	269	4.50%	82.20%	13.38%	0.00%	NA
Indica I	595	90.30%	8.90%	0.84%	0.00%	NA
Indica II	465	71.40%	26.70%	1.94%	0.00%	NA
Indica III	913	68.00%	31.10%	0.88%	0.00%	NA
Indica Intermediate	786	64.50%	33.60%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.40%	0.20%	0.00%	NA
Japonica Intermediate	241	95.00%	4.60%	0.41%	0.00%	NA
VI/Aromatic	96	65.60%	22.90%	11.46%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	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
vg1005803839	C -> T	LOC_Os10g10520.1	upstream_gene_variant ; 838.0bp to feature; MODIFIER	silent_mutation	Average:35.67; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1005803839	C -> T	LOC_Os10g10520-LOC_Os10g10530	intergenic_region ; MODIFIER	silent_mutation	Average:35.67; 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
vg1005803839	NA	3.99E-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
vg1005803839	NA	4.64E-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
vg1005803839	NA	4.46E-06	mr1555_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
vg1005803839	NA	2.50E-09	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
vg1005803839	NA	5.83E-07	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
vg1005803839	NA	4.07E-06	mr1693_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
vg1005803839	NA	1.86E-10	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
vg1005803839	NA	9.24E-09	mr1741_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
vg1005803839	NA	3.80E-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
vg1005803839	NA	9.08E-06	mr1743_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
vg1005803839	NA	2.26E-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
vg1005803839	NA	7.20E-10	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