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Detailed information for vg1002424810:

Variant ID: vg1002424810 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2424810
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATATATAGTCTGCTTAAAAACAAAAACAGTGTAAGCACATGCGTGAGAATTAATATTGAATGTTACTGTTTCCAATAACAAACGATAAGCATTTGCAA[A/G]
AATACTTTGCAGCGCCATCCGTATTTAATAAGGTACAAATAAGAACACATGGTTTAGGTTCATTGAGTTTATCAAACAGAAATTTTCATGTCAAATTCCA

Reverse complement sequence

TGGAATTTGACATGAAAATTTCTGTTTGATAAACTCAATGAACCTAAACCATGTGTTCTTATTTGTACCTTATTAAATACGGATGGCGCTGCAAAGTATT[T/C]
TTGCAAATGCTTATCGTTTGTTATTGGAAACAGTAACATTCAATATTAATTCTCACGCATGTGCTTACACTGTTTTTGTTTTTAAGCAGACTATATATTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.40%	22.50%	0.08%	0.00%	NA
All Indica	2759	93.60%	6.30%	0.07%	0.00%	NA
All Japonica	1512	66.70%	33.30%	0.00%	0.00%	NA
Aus	269	1.10%	98.90%	0.00%	0.00%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	92.00%	7.90%	0.11%	0.00%	NA
Indica Intermediate	786	90.70%	9.20%	0.13%	0.00%	NA
Temperate Japonica	767	89.80%	10.20%	0.00%	0.00%	NA
Tropical Japonica	504	31.00%	69.00%	0.00%	0.00%	NA
Japonica Intermediate	241	67.60%	32.40%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	56.70%	41.10%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002424810	A -> G	LOC_Os10g04980.1	intron_variant ; MODIFIER	silent_mutation	Average:31.976; most accessible tissue: Callus, score: 69.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002424810	NA	3.13E-06	mr1029	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
vg1002424810	NA	6.77E-07	mr1042	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
vg1002424810	2.60E-06	2.59E-06	mr1043	Jap_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
vg1002424810	NA	6.15E-08	mr1156	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
vg1002424810	NA	1.02E-07	mr1179	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
vg1002424810	NA	7.55E-06	mr1189	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
vg1002424810	NA	2.16E-07	mr1194	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
vg1002424810	NA	1.68E-06	mr1213	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
vg1002424810	NA	9.76E-06	mr1295	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
vg1002424810	NA	1.33E-06	mr1502	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
vg1002424810	NA	7.31E-06	mr1588	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
vg1002424810	NA	1.62E-06	mr1625	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
vg1002424810	NA	1.24E-07	mr1736	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
vg1002424810	NA	1.47E-06	mr1912	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