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Detailed information for vg1003132211:

Variant ID: vg1003132211 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3132211
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCTAAGGCTCATCTATTAATTCCAATAAGTGCGAGACCGCACGGTCTCGTGGAATGGAAGAGCGAGACCGTTCGGTCTCGCTGAAGCAATGAGCGACA[C/T]
TGTCTAACGGCTCCTTTTCATTAGTGATTAATTACTCAATTAACAATTAACTAATAAAAAATTAGTGATTAATTATCTGATTAGCGATTAAGTAATAATT

Reverse complement sequence

AATTATTACTTAATCGCTAATCAGATAATTAATCACTAATTTTTTATTAGTTAATTGTTAATTGAGTAATTAATCACTAATGAAAAGGAGCCGTTAGACA[G/A]
TGTCGCTCATTGCTTCAGCGAGACCGAACGGTCTCGCTCTTCCATTCCACGAGACCGTGCGGTCTCGCACTTATTGGAATTAATAGATGAGCCTTAGCCC

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	69.70%	30.10%	0.19%	0.00%	NA
All Indica	2759	53.40%	46.40%	0.22%	0.00%	NA
All Japonica	1512	96.80%	3.20%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	48.70%	51.10%	0.17%	0.00%	NA
Indica II	465	56.10%	43.70%	0.22%	0.00%	NA
Indica III	913	61.60%	38.30%	0.11%	0.00%	NA
Indica Intermediate	786	45.70%	53.90%	0.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	90.90%	9.10%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	50.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	25.60%	3.33%	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
vg1003132211	C -> T	LOC_Os10g06140.1	upstream_gene_variant ; 4939.0bp to feature; MODIFIER	silent_mutation	Average:55.35; most accessible tissue: Minghui63 root, score: 82.02	N	N	N	N
vg1003132211	C -> T	LOC_Os10g06140-LOC_Os10g06160	intergenic_region ; MODIFIER	silent_mutation	Average:55.35; most accessible tissue: Minghui63 root, score: 82.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003132211	8.79E-06	8.79E-06	mr1027	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
vg1003132211	8.79E-08	NA	mr1538	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
vg1003132211	7.13E-10	2.47E-12	mr1538	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
vg1003132211	1.56E-16	4.74E-13	mr1547	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
vg1003132211	3.92E-17	5.09E-22	mr1547	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
vg1003132211	2.34E-26	1.30E-34	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
vg1003132211	3.94E-27	3.58E-37	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
vg1003132211	9.52E-07	NA	mr1538_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
vg1003132211	2.31E-11	2.42E-15	mr1538_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
vg1003132211	1.62E-18	2.49E-21	mr1547_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
vg1003132211	1.45E-20	3.72E-30	mr1547_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
vg1003132211	2.46E-41	4.42E-46	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
vg1003132211	2.13E-41	2.65E-59	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