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Detailed information for vg0217023868:

Variant ID: vg0217023868 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17023868
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCGCTGCTCACTCACTATTAAAATAGCACTTATAGCATAACTCAATTTGTAGGAAGCCATCTGACATAGATCCTTCTGGAAAAGGCCCTAAGCCGACT[G/A]
ACACAGAAACGGGTCCTTCAAAAGAAACCGGGCCGACTGCCGAAGATCGCCCGAGTGACAATTAACCAGCAACCGACAATGCAGAGACCAGCAACGAGCC

Reverse complement sequence

GGCTCGTTGCTGGTCTCTGCATTGTCGGTTGCTGGTTAATTGTCACTCGGGCGATCTTCGGCAGTCGGCCCGGTTTCTTTTGAAGGACCCGTTTCTGTGT[C/T]
AGTCGGCTTAGGGCCTTTTCCAGAAGGATCTATGTCAGATGGCTTCCTACAAATTGAGTTATGCTATAAGTGCTATTTTAATAGTGAGTGAGCAGCGATA

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	97.30%	2.30%	0.40%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	91.80%	6.90%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	79.20%	17.50%	3.37%	0.00%	NA
Japonica Intermediate	241	93.80%	5.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0217023868	G -> A	LOC_Os02g28770.1	missense_variant ; p.Asp204Asn; MODERATE	nonsynonymous_codon ; D204N	Average:50.418; most accessible tissue: Minghui63 flag leaf, score: 77.828	unknown	unknown	TOLERATED	0.70

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217023868	9.31E-07	8.27E-07	mr1076	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
vg0217023868	NA	3.48E-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
vg0217023868	1.18E-06	9.88E-08	mr1227	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
vg0217023868	3.81E-07	5.31E-08	mr1871_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