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Detailed information for vg1011082621:

Variant ID: vg1011082621 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11082621
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGCTCTACCATATTCGTTTTCATAATTTTTTTTGGAATCGAAATCGGAATCAGAAACCCGGATATGAAAACGGAATCGAATATTATCGAATACAAATA[C/T]
GGAGCGAATACGAAGCGAAACAAATACGGTGACGAATATTAATCGGAATATAAAAACCTCTCACTACTCACAAACGATTTTTGATATTGTGTTTCTAAAA

Reverse complement sequence

TTTTAGAAACACAATATCAAAAATCGTTTGTGAGTAGTGAGAGGTTTTTATATTCCGATTAATATTCGTCACCGTATTTGTTTCGCTTCGTATTCGCTCC[G/A]
TATTTGTATTCGATAATATTCGATTCCGTTTTCATATCCGGGTTTCTGATTCCGATTTCGATTCCAAAAAAAATTATGAAAACGAATATGGTAGAGCTAG

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	90.50%	9.20%	0.30%	0.02%	NA
All Indica	2759	96.40%	3.40%	0.14%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	5.90%	90.70%	2.97%	0.37%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	96.60%	3.40%	0.00%	0.00%	NA
Indica Intermediate	786	93.10%	6.60%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	19.80%	78.10%	2.08%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg1011082621	C -> T	LOC_Os10g21630.1	upstream_gene_variant ; 4102.0bp to feature; MODIFIER	silent_mutation	Average:29.32; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1011082621	C -> T	LOC_Os10g21640.1	downstream_gene_variant ; 1577.0bp to feature; MODIFIER	silent_mutation	Average:29.32; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1011082621	C -> T	LOC_Os10g21630-LOC_Os10g21640	intergenic_region ; MODIFIER	silent_mutation	Average:29.32; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1011082621	C -> DEL	N	N	silent_mutation	Average:29.32; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011082621	NA	1.79E-06	mr1262	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
vg1011082621	NA	1.11E-08	mr1585	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
vg1011082621	1.13E-06	NA	mr1134_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
vg1011082621	NA	2.28E-07	mr1522_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
vg1011082621	NA	1.63E-09	mr1585_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
vg1011082621	NA	3.93E-11	mr1942_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