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Detailed information for vg1117082364:

Variant ID: vg1117082364 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17082364
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACGATCTAGCTAGCGGCGAAACTACAATGACAGAAATAATCTAAGCAAAGTTCAGCTCTAAACGATGATGACTACTGAATAAATATGGGTAGTAACAT[C/T]
CTAGGGTTAGGCCTAGGGCGCTCACCTCCTTGGGCTTAGTACACGGCACAATAACAAGGCTCAAGATCCAAATCAGACTCGAACTAAAAGATATACGTGA

Reverse complement sequence

TCACGTATATCTTTTAGTTCGAGTCTGATTTGGATCTTGAGCCTTGTTATTGTGCCGTGTACTAAGCCCAAGGAGGTGAGCGCCCTAGGCCTAACCCTAG[G/A]
ATGTTACTACCCATATTTATTCAGTAGTCATCATCGTTTAGAGCTGAACTTTGCTTAGATTATTTCTGTCATTGTAGTTTCGCCGCTAGCTAGATCGTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.70%	17.20%	0.11%	0.00%	NA
All Indica	2759	97.80%	2.20%	0.04%	0.00%	NA
All Japonica	1512	58.90%	40.90%	0.20%	0.00%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	93.40%	6.60%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.60%	2.30%	0.13%	0.00%	NA
Temperate Japonica	767	86.80%	13.00%	0.13%	0.00%	NA
Tropical Japonica	504	31.90%	67.70%	0.40%	0.00%	NA
Japonica Intermediate	241	26.10%	73.90%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	80.00%	18.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117082364	C -> T	LOC_Os11g29410.1	upstream_gene_variant ; 3273.0bp to feature; MODIFIER	silent_mutation	Average:38.919; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg1117082364	C -> T	LOC_Os11g29420.1	upstream_gene_variant ; 973.0bp to feature; MODIFIER	silent_mutation	Average:38.919; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg1117082364	C -> T	LOC_Os11g29420-LOC_Os11g29430	intergenic_region ; MODIFIER	silent_mutation	Average:38.919; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117082364	NA	4.89E-07	mr1243	Jap_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
vg1117082364	NA	5.73E-06	mr1282	Jap_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
vg1117082364	NA	2.28E-06	mr1730_2	Jap_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