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Detailed information for vg0322035566:

Variant ID: vg0322035566 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22035566
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTTAAAGTGCGGGGGCTACGATTCCTAGCTCTCTCCTAGCCCTGCGTCAAGCTCTGGGCGCCGTCGACGCCCGGGGCCCCCTGTGCTGGCTCTTCC[G/A]
TAGTGGTTGGCTCTAGCCCCGCCGGCTGGCTACAGTGCCTAGCTTGGCTTGATCGCGGGTGAAGATTGCTGGCTATGGAAAGTTCAGTCCTCACGCTCAC

Reverse complement sequence

GTGAGCGTGAGGACTGAACTTTCCATAGCCAGCAATCTTCACCCGCGATCAAGCCAAGCTAGGCACTGTAGCCAGCCGGCGGGGCTAGAGCCAACCACTA[C/T]
GGAAGAGCCAGCACAGGGGGCCCCGGGCGTCGACGGCGCCCAGAGCTTGACGCAGGGCTAGGAGAGAGCTAGGAATCGTAGCCCCCGCACTTTAAGCAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	34.00%	0.11%	0.28%	NA
All Indica	2759	96.50%	3.20%	0.00%	0.29%	NA
All Japonica	1512	2.10%	97.60%	0.13%	0.13%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	96.10%	3.50%	0.00%	0.34%	NA
Indica II	465	96.80%	3.00%	0.00%	0.22%	NA
Indica III	913	98.70%	1.10%	0.00%	0.22%	NA
Indica Intermediate	786	94.10%	5.50%	0.00%	0.38%	NA
Temperate Japonica	767	0.30%	99.50%	0.13%	0.13%	NA
Tropical Japonica	504	5.00%	94.80%	0.00%	0.20%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	52.20%	42.20%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322035566	G -> A	LOC_Os03g39640-LOC_Os03g39650	intergenic_region ; MODIFIER	silent_mutation	Average:68.843; most accessible tissue: Zhenshan97 flag leaf, score: 82.874	N	N	N	N
vg0322035566	G -> DEL	N	N	silent_mutation	Average:68.843; most accessible tissue: Zhenshan97 flag leaf, score: 82.874	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322035566	NA	8.22E-20	mr1588	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
vg0322035566	NA	7.53E-21	mr1689	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
vg0322035566	2.24E-14	8.65E-86	mr1718	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
vg0322035566	2.15E-13	8.44E-18	mr1718	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
vg0322035566	1.73E-13	3.66E-123	mr1750	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
vg0322035566	7.36E-16	1.11E-24	mr1750	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
vg0322035566	NA	4.71E-35	mr1828	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
vg0322035566	9.31E-07	9.31E-07	mr1987	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
vg0322035566	2.88E-07	NA	mr1718_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
vg0322035566	NA	2.46E-12	mr1718_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
vg0322035566	1.03E-08	NA	mr1750_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
vg0322035566	5.66E-08	1.46E-26	mr1750_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
vg0322035566	NA	1.83E-65	mr1828_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
vg0322035566	NA	8.27E-08	mr1987_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