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Detailed information for vg1020009101:

Variant ID: vg1020009101 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20009101
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATTCTCCCGTACTACTACTGATTAAGGCGTGCTTTTTGTTGGAATTAATGAATGGGCCTTAGCCCACTCGAAGATTAATTCTTTGGAAAATCACAAAAG[C/G]
CCACCTCATGGGATGGCATGCATGTGGAGTTTAGTACCACATTGCTTATTCTAGGAGAGAGGGACCTCCTTAAAAGGGAGGATGCCCTCCTAGCCACTTG

Reverse complement sequence

CAAGTGGCTAGGAGGGCATCCTCCCTTTTAAGGAGGTCCCTCTCTCCTAGAATAAGCAATGTGGTACTAAACTCCACATGCATGCCATCCCATGAGGTGG[G/C]
CTTTTGTGATTTTCCAAAGAATTAATCTTCGAGTGGGCTAAGGCCCATTCATTAATTCCAACAAAAAGCACGCCTTAATCAGTAGTAGTACGGGAGAATG

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	24.10%	0.10%	10.24%	65.49%	NA
All Indica	2759	2.50%	0.00%	15.04%	82.46%	NA
All Japonica	1512	69.10%	0.40%	2.51%	27.98%	NA
Aus	269	0.40%	0.00%	7.06%	92.57%	NA
Indica I	595	2.90%	0.00%	9.24%	87.90%	NA
Indica II	465	1.30%	0.00%	9.68%	89.03%	NA
Indica III	913	3.30%	0.00%	20.92%	75.79%	NA
Indica Intermediate	786	2.00%	0.00%	15.78%	82.19%	NA
Temperate Japonica	767	87.10%	0.00%	1.69%	11.21%	NA
Tropical Japonica	504	42.30%	1.20%	4.17%	52.38%	NA
Japonica Intermediate	241	68.00%	0.00%	1.66%	30.29%	NA
VI/Aromatic	96	2.10%	0.00%	2.08%	95.83%	NA
Intermediate	90	26.70%	0.00%	11.11%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020009101	C -> G	LOC_Os10g37340.1	upstream_gene_variant ; 4502.0bp to feature; MODIFIER	silent_mutation	Average:40.564; most accessible tissue: Zhenshan97 flower, score: 79.691	N	N	N	N
vg1020009101	C -> G	LOC_Os10g37350.1	upstream_gene_variant ; 2398.0bp to feature; MODIFIER	silent_mutation	Average:40.564; most accessible tissue: Zhenshan97 flower, score: 79.691	N	N	N	N
vg1020009101	C -> G	LOC_Os10g37340-LOC_Os10g37350	intergenic_region ; MODIFIER	silent_mutation	Average:40.564; most accessible tissue: Zhenshan97 flower, score: 79.691	N	N	N	N
vg1020009101	C -> DEL	N	N	silent_mutation	Average:40.564; most accessible tissue: Zhenshan97 flower, score: 79.691	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020009101	3.96E-06	3.96E-06	mr1270	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