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Detailed information for vg1009167831:

Variant ID: vg1009167831 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9167831
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCCCCCGAGCTCAAGTGTTGGTGACCTCGTCCTTGTCTCTTGCTTCGCGTTGCTGAGATCGTCAACAAGATGAATGGCAACGACAGCCAATGCAAGGT[T/C]
GAACCGCTGCGCCTTCCACATGGCCCATAAGGCTAGGTGCCACACCTCGGCCAGAGGTGGATATCCTGCACTCTCCCTGGTGGCTGCACACTCCTCTCCC

Reverse complement sequence

GGGAGAGGAGTGTGCAGCCACCAGGGAGAGTGCAGGATATCCACCTCTGGCCGAGGTGTGGCACCTAGCCTTATGGGCCATGTGGAAGGCGCAGCGGTTC[A/G]
ACCTTGCATTGGCTGTCGTTGCCATTCATCTTGTTGACGATCTCAGCAACGCGAAGCAAGAGACAAGGACGAGGTCACCAACACTTGAGCTCGGGGGACA

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	81.50%	18.40%	0.04%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	47.60%	52.30%	0.13%	0.00%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	21.50%	78.20%	0.26%	0.00%	NA
Tropical Japonica	504	89.90%	10.10%	0.00%	0.00%	NA
Japonica Intermediate	241	41.90%	58.10%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg1009167831	T -> C	LOC_Os10g18080.1	missense_variant ; p.Asn8Asp; MODERATE	nonsynonymous_codon	Average:74.461; most accessible tissue: Zhenshan97 young leaf, score: 91.311	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009167831	2.85E-06	4.64E-16	mr1013	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
vg1009167831	NA	5.45E-13	mr1031	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
vg1009167831	NA	1.91E-12	mr1034	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
vg1009167831	NA	8.30E-14	mr1056	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
vg1009167831	NA	8.40E-07	mr1118	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
vg1009167831	NA	6.36E-06	mr1495	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
vg1009167831	NA	6.04E-06	mr1642	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
vg1009167831	6.17E-08	1.65E-22	mr1768	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
vg1009167831	NA	1.94E-07	mr1768	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
vg1009167831	NA	1.21E-06	mr1870	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
vg1009167831	NA	5.19E-06	mr1118_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
vg1009167831	NA	8.18E-18	mr1682_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
vg1009167831	NA	2.69E-06	mr1768_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