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Detailed information for vg0808611252:

Variant ID: vg0808611252 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8611252
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTCGGCAAAATTTTTTTTAAAAAAAATGCGAGGAAAAGACTATCAGAAAAAATGCGCCATTTCTAAAAAAAATGGTTCGAAAAAACCACGCAAGAAAA[A/C]
AACACTATCTATATAAAAAAAATCGCTCTGAAAAAACTGTCAGAAAAAAGCTAAATTGATGGACGCTTAAGTCGGATAGGATCCATCGATTTTTTACCAT

Reverse complement sequence

ATGGTAAAAAATCGATGGATCCTATCCGACTTAAGCGTCCATCAATTTAGCTTTTTTCTGACAGTTTTTTCAGAGCGATTTTTTTTATATAGATAGTGTT[T/G]
TTTTCTTGCGTGGTTTTTTCGAACCATTTTTTTTAGAAATGGCGCATTTTTTCTGATAGTCTTTTCCTCGCATTTTTTTTAAAAAAAATTTTGCCGACAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.00%	14.90%	0.15%	0.00%	NA
All Indica	2759	77.50%	22.30%	0.18%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	80.20%	19.70%	0.17%	0.00%	NA
Indica II	465	92.70%	7.30%	0.00%	0.00%	NA
Indica III	913	67.50%	32.50%	0.00%	0.00%	NA
Indica Intermediate	786	78.10%	21.40%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg0808611252	A -> C	LOC_Os08g14364.1	upstream_gene_variant ; 4468.0bp to feature; MODIFIER	silent_mutation	Average:18.041; most accessible tissue: Zhenshan97 flower, score: 25.98	N	N	N	N
vg0808611252	A -> C	LOC_Os08g14360.1	downstream_gene_variant ; 2494.0bp to feature; MODIFIER	silent_mutation	Average:18.041; most accessible tissue: Zhenshan97 flower, score: 25.98	N	N	N	N
vg0808611252	A -> C	LOC_Os08g14350-LOC_Os08g14360	intergenic_region ; MODIFIER	silent_mutation	Average:18.041; most accessible tissue: Zhenshan97 flower, score: 25.98	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808611252	7.26E-06	7.40E-06	mr1847	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
vg0808611252	4.70E-06	4.70E-06	mr1847	Ind_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