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Detailed information for vg1010535541:

Variant ID: vg1010535541 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10535541
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCGTCCTCACATAACATGATCAAATTCCATAAGTCTTATATGGATACGATATTATTCCCGGGTCTATCCACATTTACCATAATTGGGAGCATTACTCT[T/A]
TTTAACAACTATCCAGTTGTTCCTCATATGATTTTGTTGGCAAAAACTCCGTGCACCAAGCAACCAGGAGTATGAACTAAACATACAAATTCAGCTCATT

Reverse complement sequence

AATGAGCTGAATTTGTATGTTTAGTTCATACTCCTGGTTGCTTGGTGCACGGAGTTTTTGCCAACAAAATCATATGAGGAACAACTGGATAGTTGTTAAA[A/T]
AGAGTAATGCTCCCAATTATGGTAAATGTGGATAGACCCGGGAATAATATCGTATCCATATAAGACTTATGGAATTTGATCATGTTATGTGAGGACGCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	23.30%	0.30%	0.87%	75.52%	NA
All Indica	2759	3.70%	0.30%	0.98%	95.07%	NA
All Japonica	1512	62.60%	0.00%	0.33%	37.04%	NA
Aus	269	1.10%	1.90%	1.86%	95.17%	NA
Indica I	595	4.90%	0.20%	1.34%	93.61%	NA
Indica II	465	3.40%	0.20%	0.65%	95.70%	NA
Indica III	913	3.50%	0.30%	0.99%	95.18%	NA
Indica Intermediate	786	3.20%	0.30%	0.89%	95.67%	NA
Temperate Japonica	767	76.10%	0.00%	0.52%	23.34%	NA
Tropical Japonica	504	48.80%	0.00%	0.00%	51.19%	NA
Japonica Intermediate	241	48.50%	0.00%	0.41%	51.04%	NA
VI/Aromatic	96	16.70%	1.00%	3.12%	79.17%	NA
Intermediate	90	37.80%	1.10%	1.11%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010535541	T -> A	LOC_Os10g20770.1	upstream_gene_variant ; 2263.0bp to feature; MODIFIER	silent_mutation	Average:9.109; most accessible tissue: Callus, score: 43.18	N	N	N	N
vg1010535541	T -> A	LOC_Os10g20770-LOC_Os10g20780	intergenic_region ; MODIFIER	silent_mutation	Average:9.109; most accessible tissue: Callus, score: 43.18	N	N	N	N
vg1010535541	T -> DEL	N	N	silent_mutation	Average:9.109; most accessible tissue: Callus, score: 43.18	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010535541	NA	1.18E-15	mr1158	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
vg1010535541	NA	3.09E-13	mr1166	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
vg1010535541	NA	2.80E-10	mr1574	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
vg1010535541	NA	4.28E-08	mr1762	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