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Detailed information for vg0703793591:

Variant ID: vg0703793591 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3793591
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTTTCGCTAGCGGTACTAAAGAGCACCAACACCAGTGAAAAAATTCACAGCCATTATAAAAATCACCATCCAACGGCCAGTAGTACTTATCCATCCAT[C/G]
CTCATCAACCAGCCTCTCCTCTCCTCTACCCCCACCAGCACTCTCTCCTCCTCCCACCCCACAGTCGGCGGTGGTGGCTCCGGCGTGGTGACAACGATGG

Reverse complement sequence

CCATCGTTGTCACCACGCCGGAGCCACCACCGCCGACTGTGGGGTGGGAGGAGGAGAGAGTGCTGGTGGGGGTAGAGGAGAGGAGAGGCTGGTTGATGAG[G/C]
ATGGATGGATAAGTACTACTGGCCGTTGGATGGTGATTTTTATAATGGCTGTGAATTTTTTCACTGGTGTTGGTGCTCTTTAGTACCGCTAGCGAAAATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.50%	20.20%	1.31%	0.00%	NA
All Indica	2759	94.40%	4.70%	0.83%	0.00%	NA
All Japonica	1512	62.10%	35.80%	2.05%	0.00%	NA
Aus	269	2.60%	95.50%	1.86%	0.00%	NA
Indica I	595	91.80%	6.60%	1.68%	0.00%	NA
Indica II	465	95.90%	3.00%	1.08%	0.00%	NA
Indica III	913	98.10%	1.60%	0.22%	0.00%	NA
Indica Intermediate	786	91.20%	8.00%	0.76%	0.00%	NA
Temperate Japonica	767	39.90%	56.50%	3.65%	0.00%	NA
Tropical Japonica	504	91.50%	8.30%	0.20%	0.00%	NA
Japonica Intermediate	241	71.40%	27.80%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	3.10%	2.08%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg0703793591	C -> G	LOC_Os07g07580.3	upstream_gene_variant ; 3719.0bp to feature; MODIFIER	silent_mutation	Average:68.966; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0703793591	C -> G	LOC_Os07g07580.1	upstream_gene_variant ; 3719.0bp to feature; MODIFIER	silent_mutation	Average:68.966; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0703793591	C -> G	LOC_Os07g07580.2	upstream_gene_variant ; 3719.0bp to feature; MODIFIER	silent_mutation	Average:68.966; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0703793591	C -> G	LOC_Os07g07570-LOC_Os07g07580	intergenic_region ; MODIFIER	silent_mutation	Average:68.966; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703793591	NA	3.79E-06	mr1030	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
vg0703793591	NA	1.88E-08	mr1045	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
vg0703793591	NA	4.46E-07	mr1053	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
vg0703793591	NA	8.96E-09	mr1137	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
vg0703793591	NA	1.11E-08	mr1157	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
vg0703793591	NA	9.71E-06	mr1164	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
vg0703793591	NA	3.17E-06	mr1183	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
vg0703793591	NA	1.24E-06	mr1206	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
vg0703793591	NA	7.09E-08	mr1229	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
vg0703793591	NA	6.80E-07	mr1330	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
vg0703793591	NA	9.78E-07	mr1503	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
vg0703793591	NA	1.72E-06	mr1596	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
vg0703793591	NA	4.86E-07	mr1748	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
vg0703793591	NA	1.04E-09	mr1763	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
vg0703793591	2.95E-06	2.94E-06	mr1814	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
vg0703793591	NA	3.76E-07	mr1880	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
vg0703793591	NA	5.30E-06	mr1906	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
vg0703793591	6.48E-06	NA	mr1912	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
vg0703793591	NA	2.92E-08	mr1137_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