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Detailed information for vg0801775717:

Variant ID: vg0801775717 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1775717
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCCAAACCAGTCCCTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGGGATGACATGACGATAGAAGAATTTGTTATTGACACC[G/A]
GTCTATCTACGGATCAATTGCTAGGAGTTGAACCAATAGAAAAGGCGGAATTGAAATACATGTATGAACTCGGTAAACCGCTTGTCAAGCCCGAGCTGGT

Reverse complement sequence

ACCAGCTCGGGCTTGACAAGCGGTTTACCGAGTTCATACATGTATTTCAATTCCGCCTTTTCTATTGGTTCAACTCCTAGCAATTGATCCGTAGATAGAC[C/T]
GGTGTCAATAACAAATTCTTCTATCGTCATGTCATCCCCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAGGGACTGGTTTGGAC

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	39.00%	0.10%	16.69%	44.16%	NA
All Indica	2759	3.00%	0.20%	26.60%	70.24%	NA
All Japonica	1512	97.90%	0.00%	0.66%	1.46%	NA
Aus	269	55.40%	0.00%	10.78%	33.83%	NA
Indica I	595	3.50%	0.20%	14.79%	81.51%	NA
Indica II	465	2.80%	0.60%	15.05%	81.51%	NA
Indica III	913	1.10%	0.00%	35.82%	63.09%	NA
Indica Intermediate	786	4.80%	0.10%	31.68%	63.36%	NA
Temperate Japonica	767	97.90%	0.00%	0.39%	1.69%	NA
Tropical Japonica	504	98.40%	0.00%	0.60%	0.99%	NA
Japonica Intermediate	241	96.70%	0.00%	1.66%	1.66%	NA
VI/Aromatic	96	91.70%	0.00%	2.08%	6.25%	NA
Intermediate	90	50.00%	1.10%	15.56%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801775717	G -> A	LOC_Os08g03730.1	missense_variant ; p.Gly685Ser; MODERATE	nonsynonymous_codon ; G685N	Average:10.887; most accessible tissue: Minghui63 root, score: 21.615	probably damaging	2.122	DELETERIOUS	0.00
vg0801775717	G -> DEL	LOC_Os08g03730.1	N	frameshift_variant	Average:10.887; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801775717	NA	7.45E-06	mr1586	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
vg0801775717	4.58E-07	2.95E-11	mr1739	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
vg0801775717	1.69E-07	1.16E-17	mr1739	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
vg0801775717	NA	1.71E-08	mr1172_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
vg0801775717	NA	9.86E-07	mr1472_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
vg0801775717	NA	1.66E-07	mr1483_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
vg0801775717	NA	2.46E-06	mr1654_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
vg0801775717	NA	5.95E-06	mr1722_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
vg0801775717	NA	1.08E-10	mr1734_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
vg0801775717	NA	1.38E-14	mr1739_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
vg0801775717	NA	1.62E-13	mr1807_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
vg0801775717	NA	6.32E-07	mr1807_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
vg0801775717	NA	1.84E-06	mr1834_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