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Detailed information for vg0715882829:

Variant ID: vg0715882829 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15882829
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCCGCTATTTATGCAGCATGCTCCTTTTCTTTTCTAAGTAGATGAATACCCTATCACGTTGCTGTGGGAAATTAAGTTGCATAATATGTATAGATAAG[G/A]
TGCAATATACTCCCTCTGTTCCACTATGTTTGACGTCCTAGGATGGTTGAAGCAAATTATGTTTAGGTGAAAATGACCATGTTGCTCCCAATCTATTACT

Reverse complement sequence

AGTAATAGATTGGGAGCAACATGGTCATTTTCACCTAAACATAATTTGCTTCAACCATCCTAGGACGTCAAACATAGTGGAACAGAGGGAGTATATTGCA[C/T]
CTTATCTATACATATTATGCAACTTAATTTCCCACAGCAACGTGATAGGGTATTCATCTACTTAGAAAAGAAAAGGAGCATGCTGCATAAATAGCGGCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	5.80%	0.32%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.14%	0.00%	NA
All Japonica	1512	83.50%	15.70%	0.73%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	98.90%	0.80%	0.38%	0.00%	NA
Temperate Japonica	767	95.30%	3.80%	0.91%	0.00%	NA
Tropical Japonica	504	64.50%	35.10%	0.40%	0.00%	NA
Japonica Intermediate	241	85.90%	13.30%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0715882829	G -> A	LOC_Os07g27310.1	upstream_gene_variant ; 1973.0bp to feature; MODIFIER	silent_mutation	Average:45.16; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0715882829	G -> A	LOC_Os07g27320.1	upstream_gene_variant ; 1528.0bp to feature; MODIFIER	silent_mutation	Average:45.16; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0715882829	G -> A	LOC_Os07g27310-LOC_Os07g27320	intergenic_region ; MODIFIER	silent_mutation	Average:45.16; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715882829	NA	9.67E-07	mr1213	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
vg0715882829	8.42E-08	6.12E-23	mr1301	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
vg0715882829	NA	5.99E-14	mr1301	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
vg0715882829	2.47E-06	3.01E-19	mr1410	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
vg0715882829	NA	7.27E-12	mr1410	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
vg0715882829	7.85E-09	1.84E-23	mr1301_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
vg0715882829	NA	2.05E-17	mr1301_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
vg0715882829	5.99E-06	1.82E-18	mr1410_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
vg0715882829	NA	2.17E-12	mr1410_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
vg0715882829	3.51E-06	1.12E-11	mr1993_2	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
vg0715882829	NA	1.70E-13	mr1993_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