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Detailed information for vg1013420246:

Variant ID: vg1013420246 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13420246
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, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTGGGGGTGTTTGCTCCTGAACTGCTTCGCGGGGTGCTTCGACAGTTGTTCCCTGCTGCGGCCTTGGGTTTTGCGCGTTGCCACGTTGCCTAATGTTT[C/T]
GGCATTGCTCCGTGGTGTGCGAAGAGCGTCCGTGAAAGGCGCAGTAGAGGTCTTTTCGGACCTTCTTGTGGGCTGGCTGCTGATGGTTGCTCGCTTGCTG

Reverse complement sequence

CAGCAAGCGAGCAACCATCAGCAGCCAGCCCACAAGAAGGTCCGAAAAGACCTCTACTGCGCCTTTCACGGACGCTCTTCGCACACCACGGAGCAATGCC[G/A]
AAACATTAGGCAACGTGGCAACGCGCAAAACCCAAGGCCGCAGCAGGGAACAACTGTCGAAGCACCCCGCGAAGCAGTTCAGGAGCAAACACCCCCAGCC

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	91.60%	8.30%	0.13%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	74.60%	25.00%	0.40%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	94.80%	5.10%	0.13%	0.00%	NA
Tropical Japonica	504	52.00%	47.40%	0.60%	0.00%	NA
Japonica Intermediate	241	57.70%	41.50%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg1013420246	C -> T	LOC_Os10g25880.1	downstream_gene_variant ; 4574.0bp to feature; MODIFIER	silent_mutation	Average:43.432; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg1013420246	C -> T	LOC_Os10g25900.1	downstream_gene_variant ; 2131.0bp to feature; MODIFIER	silent_mutation	Average:43.432; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg1013420246	C -> T	LOC_Os10g25890.1	intron_variant ; MODIFIER	silent_mutation	Average:43.432; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013420246	NA	8.87E-08	mr1156	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
vg1013420246	NA	1.15E-07	mr1179	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
vg1013420246	NA	1.55E-06	mr1263	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
vg1013420246	NA	1.55E-06	mr1451	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
vg1013420246	NA	1.74E-11	mr1668	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
vg1013420246	NA	2.12E-09	mr1668	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
vg1013420246	NA	5.07E-12	mr1871	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
vg1013420246	NA	3.11E-10	mr1980	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
vg1013420246	NA	1.97E-11	mr1533_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
vg1013420246	NA	4.47E-07	mr1668_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