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Detailed information for vg1009558279:

Variant ID: vg1009558279 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9558279
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAGGAGGAGGAGGGGGGATCAGAAGGAGGGGGCGGAATAAGAGATGGGGATAAGGACTGAATAAGGGAGTAAATAAGGTCGGTCGTCTTGGATGGCTT[C/T]
GGCTGGTTTTTTAGTGCCATTTTTAAAAAAACCGTTACCTATAATATAAATATAGGTGCCGGTTCTTAAAAACGGGACTTATAATATATTATAGGTGCCG

Reverse complement sequence

CGGCACCTATAATATATTATAAGTCCCGTTTTTAAGAACCGGCACCTATATTTATATTATAGGTAACGGTTTTTTTAAAAATGGCACTAAAAAACCAGCC[G/A]
AAGCCATCCAAGACGACCGACCTTATTTACTCCCTTATTCAGTCCTTATCCCCATCTCTTATTCCGCCCCCTCCTTCTGATCCCCCCTCCTCCTCCTCGT

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	60.60%	38.30%	0.59%	0.53%	NA
All Indica	2759	44.40%	53.80%	0.87%	0.91%	NA
All Japonica	1512	86.10%	13.70%	0.20%	0.00%	NA
Aus	269	87.70%	12.30%	0.00%	0.00%	NA
Indica I	595	28.60%	68.20%	1.18%	2.02%	NA
Indica II	465	60.90%	37.60%	0.86%	0.65%	NA
Indica III	913	40.20%	58.20%	0.88%	0.77%	NA
Indica Intermediate	786	51.50%	47.50%	0.64%	0.38%	NA
Temperate Japonica	767	94.50%	5.50%	0.00%	0.00%	NA
Tropical Japonica	504	79.40%	20.00%	0.60%	0.00%	NA
Japonica Intermediate	241	73.40%	26.60%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	58.30%	1.04%	0.00%	NA
Intermediate	90	70.00%	30.00%	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
vg1009558279	C -> T	LOC_Os10g18790.1	downstream_gene_variant ; 3615.0bp to feature; MODIFIER	silent_mutation	Average:59.15; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1009558279	C -> T	LOC_Os10g18780-LOC_Os10g18790	intergenic_region ; MODIFIER	silent_mutation	Average:59.15; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1009558279	C -> DEL	N	N	silent_mutation	Average:59.15; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009558279	1.12E-06	NA	mr1053	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
vg1009558279	8.78E-07	6.85E-07	mr1053	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
vg1009558279	1.11E-07	NA	mr1070	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
vg1009558279	1.26E-06	2.32E-06	mr1070	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
vg1009558279	6.98E-07	NA	mr1128	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
vg1009558279	8.38E-07	1.97E-07	mr1128	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
vg1009558279	2.67E-06	NA	mr1147	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
vg1009558279	9.07E-06	2.85E-06	mr1405	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
vg1009558279	NA	7.24E-06	mr1691	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
vg1009558279	NA	2.54E-08	mr1709	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
vg1009558279	NA	6.95E-10	mr1709	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
vg1009558279	NA	4.83E-06	mr1772	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
vg1009558279	NA	8.30E-09	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
vg1009558279	NA	5.23E-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
vg1009558279	NA	6.93E-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
vg1009558279	NA	2.00E-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
vg1009558279	NA	1.66E-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
vg1009558279	NA	6.70E-10	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