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Detailed information for vg0818303489:

Variant ID: vg0818303489 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18303489
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGTTACCAACCGGGACTAAAGATCGGTCAGCCACGTGGCCGGCCGAACCACCTTTAGTCCCGGTTTGTGTTACCAACCAGAACTAAAGATCGGTGCAC[T/C]
ATTTTTTTTATTTGCATGGCCCTGTTTTTTTTTTTGTTTTTTTATTTGCATGGCCCTGTTTGATTATCTTTAGCCACGTAACTTTTGCTGCACTAAAGTT

Reverse complement sequence

AACTTTAGTGCAGCAAAAGTTACGTGGCTAAAGATAATCAAACAGGGCCATGCAAATAAAAAAACAAAAAAAAAAACAGGGCCATGCAAATAAAAAAAAT[A/G]
GTGCACCGATCTTTAGTTCTGGTTGGTAACACAAACCGGGACTAAAGGTGGTTCGGCCGGCCACGTGGCTGACCGATCTTTAGTCCCGGTTGGTAACACG

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	50.90%	16.80%	3.60%	28.71%	NA
All Indica	2759	24.10%	21.70%	5.98%	48.28%	NA
All Japonica	1512	87.70%	11.60%	0.20%	0.46%	NA
Aus	269	98.10%	1.10%	0.37%	0.37%	NA
Indica I	595	49.40%	6.10%	3.19%	41.34%	NA
Indica II	465	28.00%	6.50%	14.62%	50.97%	NA
Indica III	913	4.20%	36.80%	3.72%	55.31%	NA
Indica Intermediate	786	25.70%	24.90%	5.60%	43.77%	NA
Temperate Japonica	767	98.60%	0.80%	0.26%	0.39%	NA
Tropical Japonica	504	67.70%	31.70%	0.20%	0.40%	NA
Japonica Intermediate	241	95.00%	4.10%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	64.40%	15.60%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818303489	T -> C	LOC_Os08g29770.1	upstream_gene_variant ; 1875.0bp to feature; MODIFIER	silent_mutation	Average:48.456; most accessible tissue: Zhenshan97 flower, score: 69.089	N	N	N	N
vg0818303489	T -> C	LOC_Os08g29760.1	downstream_gene_variant ; 3759.0bp to feature; MODIFIER	silent_mutation	Average:48.456; most accessible tissue: Zhenshan97 flower, score: 69.089	N	N	N	N
vg0818303489	T -> C	LOC_Os08g29760-LOC_Os08g29770	intergenic_region ; MODIFIER	silent_mutation	Average:48.456; most accessible tissue: Zhenshan97 flower, score: 69.089	N	N	N	N
vg0818303489	T -> DEL	N	N	silent_mutation	Average:48.456; most accessible tissue: Zhenshan97 flower, score: 69.089	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818303489	NA	2.74E-08	Yield	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0818303489	NA	5.51E-07	mr1047_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
vg0818303489	NA	1.90E-06	mr1870_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