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Detailed information for vg0206385997:

Variant ID: vg0206385997 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6385997
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGATCGATCTCTGAACTTTCAGAAAATGGAACTTTCTGGTGGTAACTAATATTTAACTGAGCATTAATTACTCATGTGTTCATGGCAGTGAACGGTGGC[G/A]
GCAGTATTGCGGGCATGGAGCTGCAGCAACGACGACGAGGAGGCCATGGATTGCCGGTGATGGTGAGATCAGCAGCACGGCGATCTCTCGGAGGACGATC

Reverse complement sequence

GATCGTCCTCCGAGAGATCGCCGTGCTGCTGATCTCACCATCACCGGCAATCCATGGCCTCCTCGTCGTCGTTGCTGCAGCTCCATGCCCGCAATACTGC[C/T]
GCCACCGTTCACTGCCATGAACACATGAGTAATTAATGCTCAGTTAAATATTAGTTACCACCAGAAAGTTCCATTTTCTGAAAGTTCAGAGATCGATCGA

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	54.60%	41.00%	0.21%	4.17%	NA
All Indica	2759	88.00%	8.70%	0.33%	3.01%	NA
All Japonica	1512	1.90%	97.90%	0.00%	0.20%	NA
Aus	269	27.90%	46.10%	0.00%	26.02%	NA
Indica I	595	90.10%	9.40%	0.50%	0.00%	NA
Indica II	465	87.70%	3.40%	0.00%	8.82%	NA
Indica III	913	89.80%	8.00%	0.22%	1.97%	NA
Indica Intermediate	786	84.40%	12.10%	0.51%	3.05%	NA
Temperate Japonica	767	2.30%	97.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	98.80%	0.00%	0.20%	NA
Japonica Intermediate	241	2.50%	96.70%	0.00%	0.83%	NA
VI/Aromatic	96	12.50%	49.00%	1.04%	37.50%	NA
Intermediate	90	43.30%	51.10%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206385997	G -> A	LOC_Os02g12260.1	missense_variant ; p.Gly46Ser; MODERATE	nonsynonymous_codon ; G46S	Average:61.913; most accessible tissue: Minghui63 flag leaf, score: 70.17	unknown	unknown	DELETERIOUS	0.00
vg0206385997	G -> DEL	LOC_Os02g12260.1	N	frameshift_variant	Average:61.913; most accessible tissue: Minghui63 flag leaf, score: 70.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206385997	NA	1.55E-27	mr1037	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
vg0206385997	NA	1.38E-47	mr1109	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
vg0206385997	NA	1.51E-30	mr1257	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
vg0206385997	NA	2.67E-29	mr1551	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
vg0206385997	NA	3.73E-10	mr1720	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
vg0206385997	NA	1.25E-54	mr1109_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