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Detailed information for vg0610271576:

Variant ID: vg0610271576 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10271576
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATTAATGTAAGGGTAAGGGTGAGTACTTAACGTACTCAGCGAGCTAGGGGAAAGAATGACATGTTCGGTTTAAACAAGGAGACTAGGGTTTTATTTG[C/T]
GGAAGCGGCCTTTTTGGCAAAGTGATTTATTTCACAAAACTCCTAGTGAGTCAAAATGTTAGTTGTCGGGAGGAGGCTCACGCCTCGACCCATTCCACAA

Reverse complement sequence

TTGTGGAATGGGTCGAGGCGTGAGCCTCCTCCCGACAACTAACATTTTGACTCACTAGGAGTTTTGTGAAATAAATCACTTTGCCAAAAAGGCCGCTTCC[G/A]
CAAATAAAACCCTAGTCTCCTTGTTTAAACCGAACATGTCATTCTTTCCCCTAGCTCGCTGAGTACGTTAAGTACTCACCCTTACCCTTACATTAATCTA

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	93.20%	6.60%	0.25%	0.00%	NA
All Indica	2759	92.10%	7.80%	0.11%	0.00%	NA
All Japonica	1512	94.10%	5.30%	0.60%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	91.60%	8.40%	0.00%	0.00%	NA
Indica III	913	86.40%	13.50%	0.11%	0.00%	NA
Indica Intermediate	786	93.00%	6.70%	0.25%	0.00%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	87.90%	10.30%	1.79%	0.00%	NA
Japonica Intermediate	241	95.00%	5.00%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0610271576	C -> T	LOC_Os06g17680.1	upstream_gene_variant ; 4516.0bp to feature; MODIFIER	silent_mutation	Average:40.734; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0610271576	C -> T	LOC_Os06g17690.1	downstream_gene_variant ; 538.0bp to feature; MODIFIER	silent_mutation	Average:40.734; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0610271576	C -> T	LOC_Os06g17690-LOC_Os06g17700	intergenic_region ; MODIFIER	silent_mutation	Average:40.734; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610271576	4.03E-06	NA	mr1165_2	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
vg0610271576	NA	1.94E-08	mr1850_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