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Detailed information for vg0307862708:

Variant ID: vg0307862708 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7862708
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTAATGAAAGAAGTATTTTATTTTATTGTTTTATTGCAAAGACTTGATATGTGTAGTCATTAATATGGCTAATTTTGTTTTATTACAAATGACCAAAA[C/G]
AAAAGAAAAGTTGTAGATCTTGATGAGAGGATCAACTTTGTTGTTGACCATATTTCCATTTGAAATCATTTAGTATCCGAAAATGTATTATAGCTAATAA

Reverse complement sequence

TTATTAGCTATAATACATTTTCGGATACTAAATGATTTCAAATGGAAATATGGTCAACAACAAAGTTGATCCTCTCATCAAGATCTACAACTTTTCTTTT[G/C]
TTTTGGTCATTTGTAATAAAACAAAATTAGCCATATTAATGACTACACATATCAAGTCTTTGCAATAAAACAATAAAATAAAATACTTCTTTCATTACAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	0.30%	2.54%	1.44%	NA
All Indica	2759	97.40%	0.40%	1.67%	0.58%	NA
All Japonica	1512	93.60%	0.10%	2.98%	3.37%	NA
Aus	269	92.20%	0.40%	7.43%	0.00%	NA
Indica I	595	97.50%	0.30%	1.68%	0.50%	NA
Indica II	465	93.10%	0.20%	4.52%	2.15%	NA
Indica III	913	98.70%	0.50%	0.66%	0.11%	NA
Indica Intermediate	786	98.30%	0.30%	1.15%	0.25%	NA
Temperate Japonica	767	91.00%	0.00%	2.61%	6.39%	NA
Tropical Japonica	504	94.80%	0.20%	4.96%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	92.70%	0.00%	7.29%	0.00%	NA
Intermediate	90	96.70%	0.00%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0307862708	C -> DEL	N	N	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0307862708	C -> G	LOC_Os03g14490.1	upstream_gene_variant ; 2594.0bp to feature; MODIFIER	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0307862708	C -> G	LOC_Os03g14460.1	downstream_gene_variant ; 2593.0bp to feature; MODIFIER	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0307862708	C -> G	LOC_Os03g14470.1	downstream_gene_variant ; 123.0bp to feature; MODIFIER	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0307862708	C -> G	LOC_Os03g14480.1	downstream_gene_variant ; 832.0bp to feature; MODIFIER	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0307862708	C -> G	LOC_Os03g14470-LOC_Os03g14480	intergenic_region ; MODIFIER	silent_mutation	Average:21.726; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307862708	1.81E-06	1.81E-06	mr1770	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