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Detailed information for vg0701480178:

Variant ID: vg0701480178 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1480178
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGGTTTCATCCTGGTTCCCAGCCGTCACCTGTGGTGTTGGGTGTTAGTCCGTTGGTTCCGCTGCTACTGCTGTTGTTGGTGTTTTCCTCGTCCGCGTC[G/A]
TTGGTTGCACTCGGGCTGTTCTGAGCTGCAACCTAAGTTAAGGTAAATAAGTCCTTTATTTATTTTAAGGATTGCAATGATTCATATTTGTCACCGTGGG

Reverse complement sequence

CCCACGGTGACAAATATGAATCATTGCAATCCTTAAAATAAATAAAGGACTTATTTACCTTAACTTAGGTTGCAGCTCAGAACAGCCCGAGTGCAACCAA[C/T]
GACGCGGACGAGGAAAACACCAACAACAGCAGTAGCAGCGGAACCAACGGACTAACACCCAACACCACAGGTGACGGCTGGGAACCAGGATGAAACCCTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.50%	4.30%	0.80%	35.40%	NA
All Indica	2759	71.50%	0.50%	0.65%	27.29%	NA
All Japonica	1512	47.80%	3.40%	0.93%	47.88%	NA
Aus	269	18.20%	19.30%	2.23%	60.22%	NA
Indica I	595	99.30%	0.00%	0.00%	0.67%	NA
Indica II	465	21.10%	1.10%	1.08%	76.77%	NA
Indica III	913	82.80%	0.00%	0.55%	16.65%	NA
Indica Intermediate	786	67.30%	1.10%	1.02%	30.53%	NA
Temperate Japonica	767	76.10%	5.70%	0.52%	17.60%	NA
Tropical Japonica	504	11.90%	0.60%	1.79%	85.71%	NA
Japonica Intermediate	241	32.40%	2.10%	0.41%	65.15%	NA
VI/Aromatic	96	12.50%	81.20%	0.00%	6.25%	NA
Intermediate	90	62.20%	6.70%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0701480178	G -> DEL	N	N	silent_mutation	Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg0701480178	G -> A	LOC_Os07g03650.1	upstream_gene_variant ; 1979.0bp to feature; MODIFIER	silent_mutation	Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg0701480178	G -> A	LOC_Os07g03640.1	downstream_gene_variant ; 3461.0bp to feature; MODIFIER	silent_mutation	Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg0701480178	G -> A	LOC_Os07g03650-LOC_Os07g03670	intergenic_region ; MODIFIER	silent_mutation	Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701480178	NA	3.70E-08	mr1705	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
vg0701480178	NA	5.12E-07	mr1057_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
vg0701480178	2.99E-07	7.63E-14	mr1567_2	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
vg0701480178	NA	8.24E-08	mr1612_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