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Detailed information for vg0714328687:

Variant ID: vg0714328687 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14328687
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.07, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TAAACTTGGCTAACGCCGGGCGTCCGAGTATGGCGTGGTATGCTGTCTCGAAATCGGCAACTTCAAAGCTGATATTCTCTGTGCGGAAGTTTTCCCGAGT[T/G]
CCAAAAGTGACCGGGAGGGTGATCTGGCCGAGTGGAGTTGCGGATAATCCTGGAATTACTCCGTGAAAAGGTGCATTGCTGGGTTTTAGCTCGGAGCGAG

Reverse complement sequence

CTCGCTCCGAGCTAAAACCCAGCAATGCACCTTTTCACGGAGTAATTCCAGGATTATCCGCAACTCCACTCGGCCAGATCACCCTCCCGGTCACTTTTGG[A/C]
ACTCGGGAAAACTTCCGCACAGAGAATATCAGCTTTGAAGTTGCCGATTTCGAGACAGCATACCACGCCATACTCGGACGCCCGGCGTTAGCCAAGTTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.10%	0.20%	17.33%	55.40%	NA
All Indica	2759	19.10%	0.10%	19.06%	61.73%	NA
All Japonica	1512	45.80%	0.00%	4.37%	49.87%	NA
Aus	269	11.50%	0.70%	76.95%	10.78%	NA
Indica I	595	37.50%	0.00%	6.89%	55.63%	NA
Indica II	465	22.60%	0.00%	9.03%	68.39%	NA
Indica III	913	3.40%	0.30%	35.49%	60.79%	NA
Indica Intermediate	786	21.20%	0.10%	15.14%	63.49%	NA
Temperate Japonica	767	69.90%	0.00%	2.35%	27.77%	NA
Tropical Japonica	504	13.10%	0.00%	5.95%	80.95%	NA
Japonica Intermediate	241	37.30%	0.00%	7.47%	55.19%	NA
VI/Aromatic	96	3.10%	1.00%	11.46%	84.38%	NA
Intermediate	90	32.20%	1.10%	10.00%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714328687	T -> DEL	LOC_Os07g25090.1	N	frameshift_variant	Average:10.807; most accessible tissue: Callus, score: 14.207	N	N	N	N
vg0714328687	T -> G	LOC_Os07g25090.1	synonymous_variant ; p.Gly847Gly; LOW	synonymous_codon	Average:10.807; most accessible tissue: Callus, score: 14.207	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714328687	NA	4.04E-13	mr1035	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
vg0714328687	NA	2.37E-17	mr1253	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
vg0714328687	NA	7.16E-06	mr1387	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
vg0714328687	1.41E-06	1.74E-26	mr1423	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
vg0714328687	NA	1.21E-15	mr1484	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
vg0714328687	NA	3.07E-12	mr1626	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
vg0714328687	NA	1.31E-08	mr1637	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
vg0714328687	NA	2.23E-07	mr1804	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
vg0714328687	NA	3.39E-11	mr1905	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
vg0714328687	NA	1.24E-07	mr1681_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