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Detailed information for vg1012832290:

Variant ID: vg1012832290 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12832290
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTTTCCATCAAGTACTCACGGGCCCAAAACGGAGCTCGGATGCAAATTTGGCGGCCGTTTGAAGTCAACAGTGTAGCAGGTGGCCGAATCGAATTCCA[G/A]
CACTTGGAGGACTTGATCTTGATATAATCTTGTTCATCCATGATGTGAGCAATGGTTGTATCTATAGTAGCCATGGTCATATTAGATTGTTTCATGATTA

Reverse complement sequence

TAATCATGAAACAATCTAATATGACCATGGCTACTATAGATACAACCATTGCTCACATCATGGATGAACAAGATTATATCAAGATCAAGTCCTCCAAGTG[C/T]
TGGAATTCGATTCGGCCACCTGCTACACTGTTGACTTCAAACGGCCGCCAAATTTGCATCCGAGCTCCGTTTTGGGCCCGTGAGTACTTGATGGAAAGGT

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	58.00%	2.50%	3.03%	36.48%	NA
All Indica	2759	34.00%	4.00%	4.93%	57.12%	NA
All Japonica	1512	91.10%	0.10%	0.33%	8.47%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	30.60%	0.20%	4.20%	65.04%	NA
Indica II	465	28.00%	14.80%	6.02%	51.18%	NA
Indica III	913	32.20%	0.20%	4.49%	63.09%	NA
Indica Intermediate	786	42.20%	4.70%	5.34%	47.71%	NA
Temperate Japonica	767	97.50%	0.00%	0.26%	2.22%	NA
Tropical Japonica	504	84.10%	0.00%	0.60%	15.28%	NA
Japonica Intermediate	241	85.50%	0.40%	0.00%	14.11%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	72.20%	6.70%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012832290	G -> A	LOC_Os10g24920.1	synonymous_variant ; p.Cys25Cys; LOW	synonymous_codon	Average:9.858; most accessible tissue: Callus, score: 28.329	N	N	N	N
vg1012832290	G -> DEL	LOC_Os10g24920.1	N	frameshift_variant	Average:9.858; most accessible tissue: Callus, score: 28.329	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012832290	4.68E-06	NA	mr1503	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
vg1012832290	NA	5.26E-07	mr1158_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
vg1012832290	NA	6.10E-06	mr1186_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
vg1012832290	NA	1.37E-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