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Detailed information for vg0506847525:

Variant ID: vg0506847525 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6847525
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AACAGAATTGTTCGCAAGAGTAGATATTAGTCGGGATACATTGAAATCAACTTCACTAGTAGCAGGGGGTTGATCATCAAGTGAAGAGTCTGAAGTCCCA[T/C]
CCTCTTCATCAATTAGATTTCCTTTCAGTTCACCATTGTCTGCACGAGATGGCTCGCCTTCACAATGCGAGGTGCTATCCAGATTAACTGATGTGCCAGC

Reverse complement sequence

GCTGGCACATCAGTTAATCTGGATAGCACCTCGCATTGTGAAGGCGAGCCATCTCGTGCAGACAATGGTGAACTGAAAGGAAATCTAATTGATGAAGAGG[A/G]
TGGGACTTCAGACTCTTCACTTGATGATCAACCCCCTGCTACTAGTGAAGTTGATTTCAATGTATCCCGACTAATATCTACTCTTGCGAACAATTCTGTT

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	88.50%	11.40%	0.04%	0.00%	NA
All Indica	2759	82.00%	17.90%	0.07%	0.00%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	70.50%	29.20%	0.22%	0.00%	NA
Indica III	913	74.40%	25.60%	0.00%	0.00%	NA
Indica Intermediate	786	88.00%	11.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	9.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0506847525	T -> C	LOC_Os05g11980.1	missense_variant ; p.Asp619Gly; MODERATE	nonsynonymous_codon ; D619G	Average:34.312; most accessible tissue: Callus, score: 63.871	benign	1.239	TOLERATED	0.58

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506847525	3.65E-62	6.14E-112	mr1039	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
vg0506847525	1.96E-56	4.24E-93	mr1039	Ind_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
vg0506847525	6.66E-23	7.84E-39	mr1632	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
vg0506847525	2.71E-21	9.79E-30	mr1632	Ind_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
vg0506847525	2.96E-78	8.01E-121	mr1039_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
vg0506847525	1.20E-65	3.26E-99	mr1039_2	Ind_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
vg0506847525	1.57E-11	6.20E-18	mr1514_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
vg0506847525	1.60E-09	3.95E-10	mr1514_2	Ind_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
vg0506847525	1.30E-40	1.96E-61	mr1632_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
vg0506847525	9.70E-35	2.18E-49	mr1632_2	Ind_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
vg0506847525	2.11E-09	NA	mr1873_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
vg0506847525	2.74E-08	3.27E-10	mr1873_2	Ind_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