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Detailed information for vg1017076177:

Variant ID: vg1017076177 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17076177
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.07, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGATCATTATATTCTCTACCTAGAAATTCCAAAAACATGGTCCATATTCCTGTTTGTCTGAATCCCATCGGAAATCTTGGAAACCTTCGGATGAGTAA[T/C]
CGTTCAGTTCTTCAAGCATGCACTCTGAGCCACTTGAGAGGTCATCTCTCGGTAAAGAGTAGTCCATGATTTCCTTGCATCCGTCTTGATTGAAATACTG

Reverse complement sequence

CAGTATTTCAATCAAGACGGATGCAAGGAAATCATGGACTACTCTTTACCGAGAGATGACCTCTCAAGTGGCTCAGAGTGCATGCTTGAAGAACTGAACG[A/G]
TTACTCATCCGAAGGTTTCCAAGATTTCCGATGGGATTCAGACAAACAGGAATATGGACCATGTTTTTGGAATTTCTAGGTAGAGAATATAATGATCCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.70%	10.30%	0.02%	0.00%	NA
All Indica	2759	93.90%	6.10%	0.00%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	15.20%	84.80%	0.00%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	90.30%	9.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.30%	6.70%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	32.30%	67.70%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	0.00%	NA

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

Category	Variant ID	Chrom	Pos	Gene	MSU	RAP	Alt_Allele_Function	Ref_geno	Alt_geno
Heading date	vg1017076177	Chr10	17076177	Ehd1	LOC_Os10g32600	Os10g0463400	delaying heading date	T	C

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017076177	T -> C	LOC_Os10g32600.1	3_prime_UTR_variant ; 187.0bp to feature; MODIFIER	silent_mutation	Average:40.414; most accessible tissue: Callus, score: 67.836	N	N	N	N
vg1017076177	T -> C	LOC_Os10g32580.1	downstream_gene_variant ; 3556.0bp to feature; MODIFIER	silent_mutation	Average:40.414; most accessible tissue: Callus, score: 67.836	N	N	N	N
vg1017076177	T -> C	LOC_Os10g32590.1	downstream_gene_variant ; 881.0bp to feature; MODIFIER	silent_mutation	Average:40.414; most accessible tissue: Callus, score: 67.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017076177	NA	2.02E-06	mr1415	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
vg1017076177	NA	2.02E-06	mr1567	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
vg1017076177	NA	3.70E-07	mr1567_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