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Detailed information for vg0817600286:

Variant ID: vg0817600286 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17600286
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:

AGACTTATCTTTAATGACTAATGATTCTTCTCTCATCAAATTGAATCCATCAGTACTCCGTGAAATCACCAATCTTTTAACTTTTACTTCTTTAGGTCTC[C/T]
ACGCTCGCTTAGGTGTCGTTCGAGGCTCTAAATTATTACATGTTTTGTTCTCTTCATCTTCGGCCTCCTTTTCTTTTTGACCTATGGCTCGAAGACGCTG

Reverse complement sequence

CAGCGTCTTCGAGCCATAGGTCAAAAAGAAAAGGAGGCCGAAGATGAAGAGAACAAAACATGTAATAATTTAGAGCCTCGAACGACACCTAAGCGAGCGT[G/A]
GAGACCTAAAGAAGTAAAAGTTAAAAGATTGGTGATTTCACGGAGTACTGATGGATTCAATTTGATGAGAGAAGAATCATTAGTCATTAAAGATAAGTCT

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	94.20%	5.20%	0.06%	0.51%	NA
All Indica	2759	99.10%	0.00%	0.07%	0.76%	NA
All Japonica	1512	83.90%	15.90%	0.07%	0.13%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	98.70%	0.00%	0.11%	1.20%	NA
Indica Intermediate	786	98.90%	0.00%	0.13%	1.02%	NA
Temperate Japonica	767	98.70%	1.00%	0.00%	0.26%	NA
Tropical Japonica	504	62.10%	37.70%	0.20%	0.00%	NA
Japonica Intermediate	241	82.60%	17.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0817600286	C -> T	LOC_Os08g28780.1	upstream_gene_variant ; 4275.0bp to feature; MODIFIER	silent_mutation	Average:27.099; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0817600286	C -> T	LOC_Os08g28760.1	downstream_gene_variant ; 3696.0bp to feature; MODIFIER	silent_mutation	Average:27.099; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0817600286	C -> T	LOC_Os08g28770.1	intron_variant ; MODIFIER	silent_mutation	Average:27.099; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0817600286	C -> DEL	N	N	silent_mutation	Average:27.099; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817600286	NA	1.55E-06	mr1040	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
vg0817600286	NA	4.96E-10	mr1533	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
vg0817600286	NA	2.85E-06	mr1676	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
vg0817600286	NA	5.28E-12	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
vg0817600286	NA	4.25E-06	mr1040_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
vg0817600286	NA	1.65E-06	mr1362_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
vg0817600286	5.28E-08	1.81E-08	mr1836_2	Jap_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