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Detailed information for vg0710533540:

Variant ID: vg0710533540 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10533540
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTCTACTGCTGCGACGGGCCAGGACGGAAGGTGAGCAACAGCGCATCCTCCGTGCTACCGACGCCGGAGGCTTCCCCCTCCTGGGGAACCACGGGCGC[G/A]
GGCTCGGCACGAGGGGTCTCGATGAAGCAAGTCCACGCCAGGGACTGACGAACAAGCTCGGGCCTGGAGGTGCTCTTGCGGGCGGTGATCTTCTGGCTGC

Reverse complement sequence

GCAGCCAGAAGATCACCGCCCGCAAGAGCACCTCCAGGCCCGAGCTTGTTCGTCAGTCCCTGGCGTGGACTTGCTTCATCGAGACCCCTCGTGCCGAGCC[C/T]
GCGCCCGTGGTTCCCCAGGAGGGGGAAGCCTCCGGCGTCGGTAGCACGGAGGATGCGCTGTTGCTCACCTTCCGTCCTGGCCCGTCGCAGCAGTAGACGA

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	77.60%	0.10%	6.14%	16.19%	NA
All Indica	2759	68.30%	0.10%	9.06%	22.47%	NA
All Japonica	1512	90.60%	0.00%	1.92%	7.47%	NA
Aus	269	92.90%	0.00%	2.60%	4.46%	NA
Indica I	595	46.40%	0.00%	21.01%	32.61%	NA
Indica II	465	59.10%	0.00%	4.52%	36.34%	NA
Indica III	913	88.90%	0.10%	2.96%	8.00%	NA
Indica Intermediate	786	66.40%	0.40%	9.80%	23.41%	NA
Temperate Japonica	767	83.80%	0.00%	3.00%	13.17%	NA
Tropical Japonica	504	98.20%	0.00%	0.20%	1.59%	NA
Japonica Intermediate	241	96.30%	0.00%	2.07%	1.66%	NA
VI/Aromatic	96	94.80%	1.00%	2.08%	2.08%	NA
Intermediate	90	77.80%	0.00%	2.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710533540	G -> DEL	N	N	silent_mutation	Average:16.83; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0710533540	G -> A	LOC_Os07g17810.1	downstream_gene_variant ; 3987.0bp to feature; MODIFIER	silent_mutation	Average:16.83; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0710533540	G -> A	LOC_Os07g17800.1	intron_variant ; MODIFIER	silent_mutation	Average:16.83; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710533540	3.52E-06	4.79E-06	mr1509_2	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