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Detailed information for vg1000903085:

Variant ID: vg1000903085 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 903085
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATCGGGGATTTCAGATCTGAGATGGCACGGACACTAGACAACAAGCAAAGAACAGATTTCGCAAATAGAGTTTTTAAGAGATAGTTTTCCCGCTAGG[C/T]
GCCACGACGGAACGGGCGCTACAGTTTGCTAGTACATTAACTTGTTTAATGTATTGACTCTTGCTGTTGATATAACCTTTTGTTTGCAGGTTTAGTCTTA

Reverse complement sequence

TAAGACTAAACCTGCAAACAAAAGGTTATATCAACAGCAAGAGTCAATACATTAAACAAGTTAATGTACTAGCAAACTGTAGCGCCCGTTCCGTCGTGGC[G/A]
CCTAGCGGGAAAACTATCTCTTAAAAACTCTATTTGCGAAATCTGTTCTTTGCTTGTTGTCTAGTGTCCGTGCCATCTCAGATCTGAAATCCCCGATCTA

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	90.60%	3.10%	2.60%	3.70%	NA
All Indica	2759	90.20%	5.10%	3.55%	1.12%	NA
All Japonica	1512	99.10%	0.10%	0.60%	0.13%	NA
Aus	269	46.50%	0.00%	2.23%	51.30%	NA
Indica I	595	93.90%	0.20%	4.87%	1.01%	NA
Indica II	465	68.00%	21.90%	9.68%	0.43%	NA
Indica III	913	97.70%	0.80%	0.88%	0.66%	NA
Indica Intermediate	786	91.70%	4.10%	2.04%	2.16%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	0.40%	3.73%	0.83%	NA
VI/Aromatic	96	93.80%	0.00%	4.17%	2.08%	NA
Intermediate	90	87.80%	3.30%	6.67%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000903085	C -> T	LOC_Os10g02470.1	upstream_gene_variant ; 1263.0bp to feature; MODIFIER	silent_mutation	Average:32.863; most accessible tissue: Zhenshan97 flower, score: 45.926	N	N	N	N
vg1000903085	C -> T	LOC_Os10g02450-LOC_Os10g02470	intergenic_region ; MODIFIER	silent_mutation	Average:32.863; most accessible tissue: Zhenshan97 flower, score: 45.926	N	N	N	N
vg1000903085	C -> DEL	N	N	silent_mutation	Average:32.863; most accessible tissue: Zhenshan97 flower, score: 45.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000903085	3.92E-07	3.76E-09	mr1197	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
vg1000903085	1.84E-06	1.84E-06	mr1197	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