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Detailed information for vg0704818663:

Variant ID: vg0704818663 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4818663
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTTTATTTCTAATTCTCAACCTTTCGACCACACCAGTGTTGGTAATGTAGCGAAACAAAATGTTTCCACGCCACAAAAGGTTGGTGTAGTAAAATAA[C/A]
ATTGGCACGTCAACCGTGGGTGGCGTGGAAGCATTATTCCCTCCGGTTTTATTTTAATTGACGTTTTGAACAATGACACGGTCTACAAGATATATCTTTA

Reverse complement sequence

TAAAGATATATCTTGTAGACCGTGTCATTGTTCAAAACGTCAATTAAAATAAAACCGGAGGGAATAATGCTTCCACGCCACCCACGGTTGACGTGCCAAT[G/T]
TTATTTTACTACACCAACCTTTTGTGGCGTGGAAACATTTTGTTTCGCTACATTACCAACACTGGTGTGGTCGAAAGGTTGAGAATTAGAAATAAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.60%	4.00%	1.40%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.11%	0.00%	NA
All Japonica	1512	84.00%	11.80%	4.17%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.40%	0.13%	0.00%	NA
Temperate Japonica	767	98.70%	0.30%	1.04%	0.00%	NA
Tropical Japonica	504	57.30%	33.90%	8.73%	0.00%	NA
Japonica Intermediate	241	92.90%	2.50%	4.56%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0704818663	C -> A	LOC_Os07g09190.1	upstream_gene_variant ; 2544.0bp to feature; MODIFIER	silent_mutation	Average:34.639; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0704818663	C -> A	LOC_Os07g09180-LOC_Os07g09190	intergenic_region ; MODIFIER	silent_mutation	Average:34.639; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704818663	NA	8.03E-06	mr1553_2	Jap_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
vg0704818663	1.07E-07	NA	mr1993_2	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