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Detailed information for vg1003042576:

Variant ID: vg1003042576 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3042576
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACAATATAAGTCATTTTAACATTTCCCACATTCATAGTGATATTAATGAATCTAGACATATATATCTATCTAGATTCATTAATACCAATATGAATGTG[A/G]
AAAATGCTAAAATGACTTACATTGTGAAACGAAGGAAGTAATAAACTGCCAATTCCTGCACAGGAACTGTCAGTACCAAACAAAAATGGCATACTAATTA

Reverse complement sequence

TAATTAGTATGCCATTTTTGTTTGGTACTGACAGTTCCTGTGCAGGAATTGGCAGTTTATTACTTCCTTCGTTTCACAATGTAAGTCATTTTAGCATTTT[T/C]
CACATTCATATTGGTATTAATGAATCTAGATAGATATATATGTCTAGATTCATTAATATCACTATGAATGTGGGAAATGTTAAAATGACTTATATTGTGA

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	32.50%	0.90%	2.05%	64.56%	NA
All Indica	2759	13.10%	0.00%	2.32%	84.56%	NA
All Japonica	1512	72.80%	2.90%	0.73%	23.54%	NA
Aus	269	6.70%	0.00%	2.60%	90.71%	NA
Indica I	595	5.90%	0.00%	1.01%	93.11%	NA
Indica II	465	5.80%	0.00%	1.51%	92.69%	NA
Indica III	913	24.20%	0.00%	3.40%	72.40%	NA
Indica Intermediate	786	10.10%	0.00%	2.54%	87.40%	NA
Temperate Japonica	767	61.30%	0.90%	0.39%	37.42%	NA
Tropical Japonica	504	93.70%	1.00%	0.40%	4.96%	NA
Japonica Intermediate	241	66.00%	13.30%	2.49%	18.26%	NA
VI/Aromatic	96	18.80%	0.00%	15.62%	65.62%	NA
Intermediate	90	38.90%	0.00%	0.00%	61.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003042576	A -> G	LOC_Os10g06010.1	downstream_gene_variant ; 3894.0bp to feature; MODIFIER	silent_mutation	Average:18.216; most accessible tissue: Callus, score: 45.529	N	N	N	N
vg1003042576	A -> G	LOC_Os10g06000-LOC_Os10g06010	intergenic_region ; MODIFIER	silent_mutation	Average:18.216; most accessible tissue: Callus, score: 45.529	N	N	N	N
vg1003042576	A -> DEL	N	N	silent_mutation	Average:18.216; most accessible tissue: Callus, score: 45.529	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003042576	3.69E-07	NA	mr1011	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
vg1003042576	5.79E-07	8.11E-06	mr1012	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
vg1003042576	1.35E-06	NA	mr1163	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