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Detailed information for vg0140952929:

Variant ID: vg0140952929 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 40952929
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGATTCCACTCCCGGCCAGATCTTCACCCGCGACGATGTCGACCTCCACCAATCCAACCGCCGCATCATCAGCCGAATATGCTGAGGTAAGTCCCCAT[T/C]
GGCTAGATCCCCTTTTCCGTTCATCAGACCGGTTTTCGCTCACCTTATCTTGTTTCCTTCTTCTCTATTCTTGTAGCATCTTTCCAATCTTGTTGCGGTT

Reverse complement sequence

AACCGCAACAAGATTGGAAAGATGCTACAAGAATAGAGAAGAAGGAAACAAGATAAGGTGAGCGAAAACCGGTCTGATGAACGGAAAAGGGGATCTAGCC[A/G]
ATGGGGACTTACCTCAGCATATTCGGCTGATGATGCGGCGGTTGGATTGGTGGAGGTCGACATCGTCGCGGGTGAAGATCTGGCCGGGAGTGGAATCGCC

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	62.70%	37.30%	0.02%	0.00%	NA
All Indica	2759	97.30%	2.70%	0.00%	0.00%	NA
All Japonica	1512	3.40%	96.60%	0.00%	0.00%	NA
Aus	269	68.40%	31.20%	0.37%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.40%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	55.60%	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
vg0140952929	T -> C	LOC_Os01g70740.1	upstream_gene_variant ; 3336.0bp to feature; MODIFIER	silent_mutation	Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0140952929	T -> C	LOC_Os01g70760.1	downstream_gene_variant ; 3426.0bp to feature; MODIFIER	silent_mutation	Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0140952929	T -> C	LOC_Os01g70750.1	intron_variant ; MODIFIER	silent_mutation	Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0140952929	NA	3.22E-28	mr1024	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
vg0140952929	8.71E-06	NA	mr1135	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
vg0140952929	NA	1.70E-23	mr1375	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
vg0140952929	7.32E-06	NA	mr1504	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
vg0140952929	NA	4.98E-06	mr1511	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
vg0140952929	NA	9.47E-08	mr1604	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
vg0140952929	NA	3.26E-08	mr1660	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
vg0140952929	6.39E-06	3.93E-37	mr1670	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
vg0140952929	NA	6.30E-07	mr1781	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
vg0140952929	NA	2.71E-26	mr1024_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
vg0140952929	NA	4.70E-09	mr1660_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
vg0140952929	3.53E-07	6.18E-50	mr1670_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
vg0140952929	NA	3.57E-11	mr1781_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