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Detailed information for vg0718051702:

Variant ID: vg0718051702 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 18051702
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: 0.07, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTAATCAAACGGCGGTGAGTAAGGTAGCTAGACATGTCCCACAATGTGACTTATCCATAGATGGTGATCGGCAACGAAGAAAACCAGAACAACGGGAA[C/T]
ACGACCAGCAACGGCATGGTCCCATAGAGAGAGAAACGGCAACGATGATCTCTTGTGGTGAACACAGCCGGGTGAGTACATCAAAACGTGTTCACGGACA

Reverse complement sequence

TGTCCGTGAACACGTTTTGATGTACTCACCCGGCTGTGTTCACCACAAGAGATCATCGTTGCCGTTTCTCTCTCTATGGGACCATGCCGTTGCTGGTCGT[G/A]
TTCCCGTTGTTCTGGTTTTCTTCGTTGCCGATCACCATCTATGGATAAGTCACATTGTGGGACATGTCTAGCTACCTTACTCACCGCCGTTTGATTACTG

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	49.50%	29.40%	9.54%	11.57%	NA
All Indica	2759	44.20%	46.50%	2.28%	7.00%	NA
All Japonica	1512	63.00%	0.70%	22.29%	14.02%	NA
Aus	269	9.30%	27.10%	13.75%	49.81%	NA
Indica I	595	83.00%	15.60%	0.17%	1.18%	NA
Indica II	465	18.50%	77.60%	1.72%	2.15%	NA
Indica III	913	31.50%	56.10%	3.83%	8.54%	NA
Indica Intermediate	786	44.80%	40.30%	2.42%	12.47%	NA
Temperate Japonica	767	66.90%	0.50%	22.03%	10.56%	NA
Tropical Japonica	504	54.20%	0.80%	26.98%	18.06%	NA
Japonica Intermediate	241	68.90%	1.20%	13.28%	16.60%	NA
VI/Aromatic	96	88.50%	1.00%	8.33%	2.08%	NA
Intermediate	90	63.30%	23.30%	6.67%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0718051702	C -> DEL	N	N	silent_mutation	Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068	N	N	N	N
vg0718051702	C -> T	LOC_Os07g30510.1	upstream_gene_variant ; 592.0bp to feature; MODIFIER	silent_mutation	Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068	N	N	N	N
vg0718051702	C -> T	LOC_Os07g30510-LOC_Os07g30530	intergenic_region ; MODIFIER	silent_mutation	Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0718051702	7.86E-07	2.71E-07	mr1211	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
vg0718051702	NA	6.20E-06	mr1184_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