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Detailed information for vg1014249003:

Variant ID: vg1014249003 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14249003
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGGCTGTCTTGGGGATGTCGGTCGGGTTCATGTGGATCTGGTGATAGCCGGAATATGCATCTAGGAAGCTCATGAGCTCGCAGCCAGCTGTTGAATCC[A/T]
CGAGATGGTCGATCCGTGGTAAGGGGAAATCGTCCTTCGGACATGCTTTGTTTAGGTCTGTGAAATCAACACATATGCGCCATTTGCCGTTTGACTTCCG

Reverse complement sequence

CGGAAGTCAAACGGCAAATGGCGCATATGTGTTGATTTCACAGACCTAAACAAAGCATGTCCGAAGGACGATTTCCCCTTACCACGGATCGACCATCTCG[T/A]
GGATTCAACAGCTGGCTGCGAGCTCATGAGCTTCCTAGATGCATATTCCGGCTATCACCAGATCCACATGAACCCGACCGACATCCCCAAGACAGCCTTT

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	49.60%	44.50%	1.61%	4.34%	NA
All Indica	2759	74.90%	18.60%	2.10%	4.46%	NA
All Japonica	1512	0.50%	94.90%	0.93%	3.64%	NA
Aus	269	91.40%	8.20%	0.37%	0.00%	NA
Indica I	595	58.50%	36.80%	2.52%	2.18%	NA
Indica II	465	78.70%	12.70%	2.80%	5.81%	NA
Indica III	913	84.90%	7.40%	1.64%	6.02%	NA
Indica Intermediate	786	73.40%	21.10%	1.91%	3.56%	NA
Temperate Japonica	767	0.10%	96.30%	0.52%	3.00%	NA
Tropical Japonica	504	0.80%	92.70%	1.39%	5.16%	NA
Japonica Intermediate	241	1.20%	95.00%	1.24%	2.49%	NA
VI/Aromatic	96	2.10%	78.10%	2.08%	17.71%	NA
Intermediate	90	22.20%	65.60%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014249003	A -> T	LOC_Os10g27030.1	downstream_gene_variant ; 4128.0bp to feature; MODIFIER	silent_mutation	Average:21.982; most accessible tissue: Callus, score: 44.448	N	N	N	N
vg1014249003	A -> T	LOC_Os10g27040.1	intron_variant ; MODIFIER	silent_mutation	Average:21.982; most accessible tissue: Callus, score: 44.448	N	N	N	N
vg1014249003	A -> DEL	N	N	silent_mutation	Average:21.982; most accessible tissue: Callus, score: 44.448	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014249003	4.85E-06	NA	mr1839	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