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Detailed information for vg0818442017:

Variant ID: vg0818442017 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18442017
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.25, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGGGTTGTTTATTTGAATATCCGAGTTTATTCCATGACTATGACTTCTAGATGGATACTGTACGTATGTAATACTATTGTTTGCTGCTAATGAGTCAA[A/G]
TTGGAGATAGCTTGGTCTCGGAATATGGTTTCTTTGTTTGTTCCATGTGTAGGTGACTCGATGTCTCGGGAGAGTATTTGCGGTGATGGACCGGGAGTCA

Reverse complement sequence

TGACTCCCGGTCCATCACCGCAAATACTCTCCCGAGACATCGAGTCACCTACACATGGAACAAACAAAGAAACCATATTCCGAGACCAAGCTATCTCCAA[T/C]
TTGACTCATTAGCAGCAAACAATAGTATTACATACGTACAGTATCCATCTAGAAGTCATAGTCATGGAATAAACTCGGATATTCAAATAAACAACCCGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.10%	7.00%	0.99%	2.86%	NA
All Indica	2759	84.00%	11.90%	0.80%	3.33%	NA
All Japonica	1512	97.80%	0.00%	1.52%	0.66%	NA
Aus	269	87.70%	0.40%	0.74%	11.15%	NA
Indica I	595	82.20%	5.90%	1.51%	10.42%	NA
Indica II	465	96.80%	2.20%	0.00%	1.08%	NA
Indica III	913	83.10%	15.90%	0.66%	0.33%	NA
Indica Intermediate	786	78.80%	17.60%	0.89%	2.80%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	95.20%	0.00%	3.37%	1.39%	NA
Japonica Intermediate	241	96.30%	0.00%	2.49%	1.24%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818442017	A -> G	LOC_Os08g30010.1	downstream_gene_variant ; 3573.0bp to feature; MODIFIER	silent_mutation	Average:53.795; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0818442017	A -> G	LOC_Os08g30010-LOC_Os08g30014	intergenic_region ; MODIFIER	silent_mutation	Average:53.795; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0818442017	A -> DEL	N	N	silent_mutation	Average:53.795; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818442017	4.11E-07	4.11E-07	mr1066	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
vg0818442017	NA	1.19E-06	mr1177	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
vg0818442017	7.38E-06	7.38E-06	mr1571	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
vg0818442017	NA	6.33E-06	mr1639	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