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Detailed information for vg0703303192:

Variant ID: vg0703303192 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3303192
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGATGATGCAATTGCACATGTGGACCTCATGTGTGATGCAATCGACGTGCCGGCCCATATCGATCCATGGGTCTCATCGGTTGCACATATTTCCTAAT[A/C]
AGCCGTTTTGGCTTATATGTAACTCAAGTTGCACAAATTAATTTATATGTAAAACTTTTATATATTTGTTCGTAGAGATTTAAAAGCCAACGCTAAAAAG

Reverse complement sequence

CTTTTTAGCGTTGGCTTTTAAATCTCTACGAACAAATATATAAAAGTTTTACATATAAATTAATTTGTGCAACTTGAGTTACATATAAGCCAAAACGGCT[T/G]
ATTAGGAAATATGTGCAACCGATGAGACCCATGGATCGATATGGGCCGGCACGTCGATTGCATCACACATGAGGTCCACATGTGCAATTGCATCATCTGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	5.00%	0.13%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	84.90%	14.80%	0.33%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	57.90%	41.50%	0.60%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0703303192	A -> C	LOC_Os07g06770.1	upstream_gene_variant ; 3595.0bp to feature; MODIFIER	silent_mutation	Average:61.996; most accessible tissue: Callus, score: 90.955	N	N	N	N
vg0703303192	A -> C	LOC_Os07g06760.1	downstream_gene_variant ; 1127.0bp to feature; MODIFIER	silent_mutation	Average:61.996; most accessible tissue: Callus, score: 90.955	N	N	N	N
vg0703303192	A -> C	LOC_Os07g06760-LOC_Os07g06770	intergenic_region ; MODIFIER	silent_mutation	Average:61.996; most accessible tissue: Callus, score: 90.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703303192	NA	4.99E-06	mr1083	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
vg0703303192	3.72E-06	3.72E-06	mr1131	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