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Detailed information for vg1000766238:

Variant ID: vg1000766238 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 766238
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAATCAGTCACATTGCAGGTATTCTCTTTATTTAATAACTAGTATGGTGGTCCGCGCAGATTGTGCGGCTAGCATCATTATATTTTCTCTCATATAATA[G/A]
CATATATATTTTCTCAATGTATTATTCAAATATGTTAAAATGGCAACATAATTTTAAATTTTGTACTATCTTTACGAAACTACTAATGTGTAATATTCAT

Reverse complement sequence

ATGAATATTACACATTAGTAGTTTCGTAAAGATAGTACAAAATTTAAAATTATGTTGCCATTTTAACATATTTGAATAATACATTGAGAAAATATATATG[C/T]
TATTATATGAGAGAAAATATAATGATGCTAGCCGCACAATCTGCGCGGACCACCATACTAGTTATTAAATAAAGAGAATACCTGCAATGTGACTGATTCC

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	73.20%	6.20%	18.39%	2.20%	NA
All Indica	2759	81.10%	1.00%	16.53%	1.34%	NA
All Japonica	1512	56.90%	13.00%	25.86%	4.30%	NA
Aus	269	94.10%	5.90%	0.00%	0.00%	NA
Indica I	595	84.70%	0.00%	13.95%	1.34%	NA
Indica II	465	73.80%	0.00%	24.95%	1.29%	NA
Indica III	913	79.00%	2.60%	16.54%	1.86%	NA
Indica Intermediate	786	85.20%	0.50%	13.49%	0.76%	NA
Temperate Japonica	767	72.50%	19.00%	7.04%	1.43%	NA
Tropical Japonica	504	33.90%	2.00%	54.76%	9.33%	NA
Japonica Intermediate	241	55.20%	16.60%	25.31%	2.90%	NA
VI/Aromatic	96	56.20%	43.80%	0.00%	0.00%	NA
Intermediate	90	58.90%	14.40%	24.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000766238	G -> A	LOC_Os10g02210.1	upstream_gene_variant ; 926.0bp to feature; MODIFIER	silent_mutation	Average:45.595; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg1000766238	G -> A	LOC_Os10g02210-LOC_Os10g02220	intergenic_region ; MODIFIER	silent_mutation	Average:45.595; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg1000766238	G -> DEL	N	N	silent_mutation	Average:45.595; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000766238	NA	4.15E-10	mr1549	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
vg1000766238	6.12E-06	NA	mr1757	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
vg1000766238	NA	5.81E-09	mr1757	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
vg1000766238	1.43E-07	NA	mr1549_2	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
vg1000766238	NA	2.05E-09	mr1549_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
vg1000766238	7.15E-07	NA	mr1757_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
vg1000766238	NA	6.30E-09	mr1757_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