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Detailed information for vg1012521610:

Variant ID: vg1012521610 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12521610
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTTGTACTCAGTCTTGCTCAATTTTTCCCAAACCCAGAAGAGGAGCCCCTTGAAGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCT[A/G]
TGGTCGTCGCCCTAGTCTTCCACTGTTTCTCGTTTGTCTTTGTGTGTGCTGGGCCTTCGCTACCCATGTAATAAATTAACTATTTACGCTTCCGCTTGTT

Reverse complement sequence

AACAAGCGGAAGCGTAAATAGTTAATTTATTACATGGGTAGCGAAGGCCCAGCACACACAAAGACAAACGAGAAACAGTGGAAGACTAGGGCGACGACCA[T/C]
AGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCTTCAAGGGGCTCCTCTTCTGGGTTTGGGAAAAATTGAGCAAGACTGAGTACAACCA

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	30.70%	0.10%	6.07%	63.06%	NA
All Indica	2759	2.30%	0.10%	4.17%	93.40%	NA
All Japonica	1512	88.70%	0.00%	0.73%	10.58%	NA
Aus	269	3.00%	0.00%	32.34%	64.68%	NA
Indica I	595	2.20%	0.20%	3.19%	94.45%	NA
Indica II	465	2.60%	0.00%	3.01%	94.41%	NA
Indica III	913	1.40%	0.20%	5.59%	92.77%	NA
Indica Intermediate	786	3.20%	0.10%	3.94%	92.75%	NA
Temperate Japonica	767	97.00%	0.00%	0.13%	2.87%	NA
Tropical Japonica	504	80.20%	0.00%	1.19%	18.65%	NA
Japonica Intermediate	241	80.10%	0.00%	1.66%	18.26%	NA
VI/Aromatic	96	5.20%	2.10%	68.75%	23.96%	NA
Intermediate	90	38.90%	1.10%	8.89%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012521610	A -> G	LOC_Os10g24420.1	intron_variant ; MODIFIER	silent_mutation	Average:6.767; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1012521610	A -> DEL	N	N	silent_mutation	Average:6.767; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012521610	3.00E-06	NA	mr1141	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