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Detailed information for vg0704746642:

Variant ID: vg0704746642 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4746642
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATTTTTGATGGATTCGGTGCTTGATGCAGATCGGTAAGGCCGAGAAGTCAAGAACTTGAGCTACGCTTGCAAAACTTGATAAATGAATCATATTACTA[C/T]
GGTTAGTAATCAAAGCTAGAAATCATGTGCTTATTATATTAAACAAATAGAGAATCCCACGTATGTAGCTGCAGATTTCCCTAGATTCTACCAAGAAAAC

Reverse complement sequence

GTTTTCTTGGTAGAATCTAGGGAAATCTGCAGCTACATACGTGGGATTCTCTATTTGTTTAATATAATAAGCACATGATTTCTAGCTTTGATTACTAACC[G/A]
TAGTAATATGATTCATTTATCAAGTTTTGCAAGCGTAGCTCAAGTTCTTGACTTCTCGGCCTTACCGATCTGCATCAAGCACCGAATCCATCAAAAATCA

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	97.40%	1.60%	0.99%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.20%	4.80%	3.04%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.60%	8.10%	5.35%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	95.00%	3.30%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0704746642	C -> T	LOC_Os07g09070.1	upstream_gene_variant ; 1936.0bp to feature; MODIFIER	silent_mutation	Average:56.976; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0704746642	C -> T	LOC_Os07g09080.1	upstream_gene_variant ; 3605.0bp to feature; MODIFIER	silent_mutation	Average:56.976; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0704746642	C -> T	LOC_Os07g09070-LOC_Os07g09080	intergenic_region ; MODIFIER	silent_mutation	Average:56.976; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704746642	2.41E-06	5.41E-07	mr1550	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