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Detailed information for vg0307680956:

Variant ID: vg0307680956 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7680956
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAGCCCAAAGAGAAACTTTAGATACCATATGTAACATCCCGGCCTAGGGCTTAATAAGATTAATAGAATACTCATATCAACAAGTTGCAACTTCTTTTC[C/T]
GGAAGCCAATCTCCAAAGAACTCTAGGGTTAAGCGATTCTTCCCGGGTGCACACGAGTGGGGACAAAGTGTTGCAGAAAAGACATGTGTTGGTCTGTGAG

Reverse complement sequence

CTCACAGACCAACACATGTCTTTTCTGCAACACTTTGTCCCCACTCGTGTGCACCCGGGAAGAATCGCTTAACCCTAGAGTTCTTTGGAGATTGGCTTCC[G/A]
GAAAAGAAGTTGCAACTTGTTGATATGAGTATTCTATTAATCTTATTAAGCCCTAGGCCGGGATGTTACATATGGTATCTAAAGTTTCTCTTTGGGCTTA

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	46.40%	19.80%	12.61%	21.20%	NA
All Indica	2759	26.70%	31.10%	19.25%	22.94%	NA
All Japonica	1512	81.50%	1.20%	1.72%	15.61%	NA
Aus	269	59.10%	15.60%	10.41%	14.87%	NA
Indica I	595	19.70%	24.00%	29.41%	26.89%	NA
Indica II	465	26.50%	32.30%	21.51%	19.78%	NA
Indica III	913	33.50%	33.40%	13.03%	20.04%	NA
Indica Intermediate	786	24.40%	33.00%	17.43%	25.19%	NA
Temperate Japonica	767	79.80%	1.30%	0.91%	17.99%	NA
Tropical Japonica	504	79.40%	1.20%	1.59%	17.86%	NA
Japonica Intermediate	241	91.30%	0.80%	4.56%	3.32%	NA
VI/Aromatic	96	16.70%	8.30%	2.08%	72.92%	NA
Intermediate	90	51.10%	13.30%	10.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0307680956	C -> T	LOC_Os03g14130.1	upstream_gene_variant ; 3831.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14140.1	upstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14160.1	upstream_gene_variant ; 2459.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14120.1	downstream_gene_variant ; 4102.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14150.1	downstream_gene_variant ; 568.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14120.2	downstream_gene_variant ; 4721.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14120.3	downstream_gene_variant ; 4721.0bp to feature; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> T	LOC_Os03g14140-LOC_Os03g14150	intergenic_region ; MODIFIER	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0307680956	C -> DEL	N	N	silent_mutation	Average:37.738; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307680956	NA	2.23E-06	mr1510	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
vg0307680956	5.54E-07	5.54E-07	mr1802	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