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Detailed information for vg1000984389:

Variant ID: vg1000984389 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 984389
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAAGCAGGGACCAGTATATATCAATATATGTATACCATACCGAAATAGCAAGGCAGTAATTACCTCAGAGATATCCCTCAATGTCAACAAGATTAGA[T/C]
GCATACTATTTTTCATTTGGATGTATACATATAAAACTAATCACATAGTGCAACTTAGGAAAACTGAATTTCAGTTTGGATCACATTGTTTCTAAGCTTT

Reverse complement sequence

AAAGCTTAGAAACAATGTGATCCAAACTGAAATTCAGTTTTCCTAAGTTGCACTATGTGATTAGTTTTATATGTATACATCCAAATGAAAAATAGTATGC[A/G]
TCTAATCTTGTTGACATTGAGGGATATCTCTGAGGTAATTACTGCCTTGCTATTTCGGTATGGTATACATATATTGATATATACTGGTCCCTGCTTAATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.00%	5.40%	16.04%	0.51%	NA
All Indica	2759	67.20%	7.90%	24.54%	0.36%	NA
All Japonica	1512	95.40%	1.00%	3.44%	0.13%	NA
Aus	269	87.00%	7.10%	3.72%	2.23%	NA
Indica I	595	67.20%	4.70%	28.07%	0.00%	NA
Indica II	465	60.90%	8.60%	30.54%	0.00%	NA
Indica III	913	68.20%	9.60%	21.14%	0.99%	NA
Indica Intermediate	786	69.60%	8.00%	22.26%	0.13%	NA
Temperate Japonica	767	99.10%	0.00%	0.91%	0.00%	NA
Tropical Japonica	504	90.70%	2.20%	7.14%	0.00%	NA
Japonica Intermediate	241	93.80%	1.70%	3.73%	0.83%	NA
VI/Aromatic	96	92.70%	0.00%	2.08%	5.21%	NA
Intermediate	90	76.70%	3.30%	18.89%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000984389	T -> C	LOC_Os10g02584-LOC_Os10g02600	intergenic_region ; MODIFIER	silent_mutation	Average:20.135; most accessible tissue: Callus, score: 28.08	N	N	N	N
vg1000984389	T -> DEL	N	N	silent_mutation	Average:20.135; most accessible tissue: Callus, score: 28.08	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000984389	3.73E-06	NA	mr1532	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