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Detailed information for vg0334582408:

Variant ID: vg0334582408 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34582408
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTATCTATAACCCTGACAGCACTCATAGAAAGCAAGACACCTATAGTGATTTTATCAATATAAGATATGCCTCGAGGGTGCTCATAGGACGCTCTGCAT[G/A]
CTCATTTTCCCTCCTCTCTCTAGATACCTAGTATTGATGGCTGCATGTTTCATACAAAGAATAAAGCTCCTTAGCAAGCTTTAATTTTTTTCCCTTAAAA

Reverse complement sequence

TTTTAAGGGAAAAAAATTAAAGCTTGCTAAGGAGCTTTATTCTTTGTATGAAACATGCAGCCATCAATACTAGGTATCTAGAGAGAGGAGGGAAAATGAG[C/T]
ATGCAGAGCGTCCTATGAGCACCCTCGAGGCATATCTTATATTGATAAAATCACTATAGGTGTCTTGCTTTCTATGAGTGCTGTCAGGGTTATAGATACC

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	94.90%	5.10%	0.04%	0.00%	NA
All Indica	2759	91.70%	8.30%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	80.70%	19.10%	0.22%	0.00%	NA
Indica Intermediate	786	94.40%	5.60%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0334582408	G -> A	LOC_Os03g60850-LOC_Os03g60870	intergenic_region ; MODIFIER	silent_mutation	Average:43.814; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334582408	6.59E-06	3.63E-09	mr1970	Ind_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
vg0334582408	4.17E-06	1.39E-10	mr1973	Ind_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
vg0334582408	NA	1.98E-07	mr1798_2	Ind_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
vg0334582408	1.66E-06	2.21E-10	mr1970_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
vg0334582408	3.06E-06	1.27E-12	mr1973_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