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Detailed information for vg1011491998:

Variant ID: vg1011491998 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11491998
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTGGTACTTCGAGAAGCCACCCCTGACTGCCGAGTTCCTTACGACAGCCCATCATGGCCATACAACCAGGGCTAAATACGGAGGAATACCCTCCCCAGG[G/A]
AATTAACTTAGAATTATATACACGCGCGGAGGAATACCCGTACTGAGCTGTCACCATCAGTGACCCACCTCTCATCCGCTGCATATAACCCCAAATAATG

Reverse complement sequence

CATTATTTGGGGTTATATGCAGCGGATGAGAGGTGGGTCACTGATGGTGACAGCTCAGTACGGGTATTCCTCCGCGCGTGTATATAATTCTAAGTTAATT[C/T]
CCTGGGGAGGGTATTCCTCCGTATTTAGCCCTGGTTGTATGGCCATGATGGGCTGTCGTAAGGAACTCGGCAGTCAGGGGTGGCTTCTCGAAGTACCAGG

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	40.10%	4.10%	27.00%	28.76%	NA
All Indica	2759	34.30%	1.50%	29.87%	34.36%	NA
All Japonica	1512	54.50%	6.60%	15.94%	22.95%	NA
Aus	269	22.30%	11.90%	48.33%	17.47%	NA
Indica I	595	49.60%	0.50%	17.14%	32.77%	NA
Indica II	465	31.80%	1.50%	24.95%	41.72%	NA
Indica III	913	27.80%	1.90%	39.98%	30.34%	NA
Indica Intermediate	786	31.60%	1.90%	30.66%	35.88%	NA
Temperate Japonica	767	84.70%	1.40%	8.21%	5.61%	NA
Tropical Japonica	504	18.70%	12.50%	22.82%	46.03%	NA
Japonica Intermediate	241	33.20%	10.80%	26.14%	29.88%	NA
VI/Aromatic	96	27.10%	11.50%	57.29%	4.17%	NA
Intermediate	90	46.70%	10.00%	28.89%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011491998	G -> A	LOC_Os10g22210.1	upstream_gene_variant ; 913.0bp to feature; MODIFIER	silent_mutation	Average:11.206; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1011491998	G -> A	LOC_Os10g22220.1	downstream_gene_variant ; 2753.0bp to feature; MODIFIER	silent_mutation	Average:11.206; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1011491998	G -> A	LOC_Os10g22210-LOC_Os10g22220	intergenic_region ; MODIFIER	silent_mutation	Average:11.206; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1011491998	G -> DEL	N	N	silent_mutation	Average:11.206; 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
vg1011491998	5.70E-07	NA	mr1354	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