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Detailed information for vg0620951869:

Variant ID: vg0620951869 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20951869
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.08, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCAAGTGTTGCTATTAGAGATTGATGAAGTATATCCCAGTGCTGCTATTTCAAGGAGCTTCCACGCATTGATTATTAGTTAGGCATTCCCAAGCATA[C/T]
GCAAATCATGCTTAGATACAAAGAAAAAGTAAACACATCTCTTTATCTTTCTTCATAGTGTAGCATATGCATCTAAAGAAATCGACAGACCAAAGTAGTT

Reverse complement sequence

AACTACTTTGGTCTGTCGATTTCTTTAGATGCATATGCTACACTATGAAGAAAGATAAAGAGATGTGTTTACTTTTTCTTTGTATCTAAGCATGATTTGC[G/A]
TATGCTTGGGAATGCCTAACTAATAATCAATGCGTGGAAGCTCCTTGAAATAGCAGCACTGGGATATACTTCATCAATCTCTAATAGCAACACTTGGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.80%	22.90%	0.19%	0.08%	NA
All Indica	2759	73.00%	26.50%	0.33%	0.14%	NA
All Japonica	1512	97.90%	2.10%	0.00%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	96.00%	4.00%	0.00%	0.00%	NA
Indica II	465	68.40%	31.20%	0.43%	0.00%	NA
Indica III	913	56.20%	43.00%	0.44%	0.33%	NA
Indica Intermediate	786	77.90%	21.60%	0.38%	0.13%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0620951869	C -> T	LOC_Os06g35920.1	upstream_gene_variant ; 1571.0bp to feature; MODIFIER	silent_mutation	Average:63.603; most accessible tissue: Minghui63 flower, score: 76.811	N	N	N	N
vg0620951869	C -> T	LOC_Os06g35910.1	intron_variant ; MODIFIER	silent_mutation	Average:63.603; most accessible tissue: Minghui63 flower, score: 76.811	N	N	N	N
vg0620951869	C -> T	LOC_Os06g35910.2	intron_variant ; MODIFIER	silent_mutation	Average:63.603; most accessible tissue: Minghui63 flower, score: 76.811	N	N	N	N
vg0620951869	C -> DEL	N	N	silent_mutation	Average:63.603; most accessible tissue: Minghui63 flower, score: 76.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620951869	1.70E-06	NA	mr1695	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
vg0620951869	NA	2.16E-08	mr1582_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