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Detailed information for vg1021305364:

Variant ID: vg1021305364 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 21305364
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTGTAGTTGTAGAATACAGAAAATAAACTAGAAGTCAGAAGCTGGGTTTCCCAGCTTCTCCAAATTCTCACCAGTTGTTTCTTAGAATCTTAAACTC[C/T]
ACCAAACAGGGCCAAGGACGATAACTATCCTTGGATTTATAGATGTGTTTTTGGTGTGTTTTACTGTACCTGCCGGAAAAAGAAACTATCCTCTGTTCGT

Reverse complement sequence

ACGAACAGAGGATAGTTTCTTTTTCCGGCAGGTACAGTAAAACACACCAAAAACACATCTATAAATCCAAGGATAGTTATCGTCCTTGGCCCTGTTTGGT[G/A]
GAGTTTAAGATTCTAAGAAACAACTGGTGAGAATTTGGAGAAGCTGGGAAACCCAGCTTCTGACTTCTAGTTTATTTTCTGTATTCTACAACTACAGTTT

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	96.00%	3.80%	0.13%	0.00%	NA
All Indica	2759	93.50%	6.30%	0.18%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.20%	0.34%	0.00%	NA
Indica II	465	74.40%	25.60%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	5.90%	0.38%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	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
vg1021305364	C -> T	LOC_Os10g39790.2	upstream_gene_variant ; 3636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021305364	C -> T	LOC_Os10g39810.1	upstream_gene_variant ; 3089.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021305364	C -> T	LOC_Os10g39790.3	upstream_gene_variant ; 3636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021305364	C -> T	LOC_Os10g39790.4	upstream_gene_variant ; 3636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021305364	C -> T	LOC_Os10g39810.2	upstream_gene_variant ; 3089.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021305364	C -> T	LOC_Os10g39800.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1021305364	NA	1.26E-06	mr1343	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
vg1021305364	4.19E-06	6.27E-07	mr1392	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
vg1021305364	8.88E-06	8.88E-06	mr1392	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
vg1021305364	NA	3.10E-06	mr1415	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
vg1021305364	NA	3.10E-06	mr1567	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
vg1021305364	NA	1.88E-09	mr1902_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