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Detailed information for vg1017360795:

Variant ID: vg1017360795 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17360795
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCGGGATCGCCCCGCCGAGCTGGTTGTCGCCGAGTTCAAGAATCCTCAATTGCGGCATCGACCCAAGGAACTCCGGGATGCCGCCGGTGAGATTGTTG[C/G]
CGGCCATCCGCAGGTCCTGCAGCTTCATCAACTTCCCGAGCGACGCCGGAATCGAGCCGGAGAACGCATTGATGGACAGGTTGAGGTACCTCAGATTCGG

Reverse complement sequence

CCGAATCTGAGGTACCTCAACCTGTCCATCAATGCGTTCTCCGGCTCGATTCCGGCGTCGCTCGGGAAGTTGATGAAGCTGCAGGACCTGCGGATGGCCG[G/C]
CAACAATCTCACCGGCGGCATCCCGGAGTTCCTTGGGTCGATGCCGCAATTGAGGATTCTTGAACTCGGCGACAACCAGCTCGGCGGGGCGATCCCGCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.10%	2.20%	10.52%	43.12%	NA
All Indica	2759	28.90%	3.40%	5.58%	62.12%	NA
All Japonica	1512	78.60%	0.50%	13.03%	7.87%	NA
Aus	269	5.90%	0.00%	39.41%	54.65%	NA
Indica I	595	8.20%	8.90%	7.56%	75.29%	NA
Indica II	465	23.00%	4.30%	3.87%	68.82%	NA
Indica III	913	43.50%	0.10%	5.70%	50.71%	NA
Indica Intermediate	786	30.90%	2.70%	4.96%	61.45%	NA
Temperate Japonica	767	97.90%	0.30%	0.39%	1.43%	NA
Tropical Japonica	504	57.70%	0.80%	34.72%	6.75%	NA
Japonica Intermediate	241	61.00%	0.40%	7.88%	30.71%	NA
VI/Aromatic	96	34.40%	1.00%	35.42%	29.17%	NA
Intermediate	90	57.80%	2.20%	6.67%	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
vg1017360795	C -> G	LOC_Os10g33130.1	missense_variant ; p.Gly276Ala; MODERATE	nonsynonymous_codon ; G276A	Average:37.719; most accessible tissue: Zhenshan97 flower, score: 75.657	benign	0.073	TOLERATED	1.00
vg1017360795	C -> DEL	LOC_Os10g33130.1	N	frameshift_variant	Average:37.719; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017360795	NA	4.27E-08	mr1038	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
vg1017360795	NA	2.08E-08	mr1038	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
vg1017360795	6.05E-06	NA	mr1344	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
vg1017360795	NA	5.72E-06	mr1344	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
vg1017360795	NA	1.13E-08	mr1389	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
vg1017360795	NA	2.70E-08	mr1389	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
vg1017360795	NA	3.64E-06	mr1518	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
vg1017360795	NA	4.80E-06	mr1534	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
vg1017360795	6.82E-06	1.40E-07	mr1716	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
vg1017360795	2.14E-06	5.23E-07	mr1745	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
vg1017360795	2.91E-06	NA	mr1798	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
vg1017360795	2.70E-06	4.22E-07	mr1798	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
vg1017360795	NA	4.33E-06	mr1974	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
vg1017360795	NA	2.38E-06	mr1974	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