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Detailed information for vg0529701170:

Variant ID: vg0529701170 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29701170
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACTTCGACAAGACAGCTCCCACTAGGAAGATCTTCAGCTCTGGTATGGGGAAAAGAGAGCAAGACTGAGTACTACCCACTGTACTCAGCAAGTCATAT[C/T]
GGAAGAGGAGGTATGATGCAGGATATAACCGAAGGAGGCTAAAGGTTCTTTTGCACAAAGCAGGCATTTAAAAACAGTAGTTGAAAGCAGTAAAACAGTT

Reverse complement sequence

AACTGTTTTACTGCTTTCAACTACTGTTTTTAAATGCCTGCTTTGTGCAAAAGAACCTTTAGCCTCCTTCGGTTATATCCTGCATCATACCTCCTCTTCC[G/A]
ATATGACTTGCTGAGTACAGTGGGTAGTACTCAGTCTTGCTCTCTTTTCCCCATACCAGAGCTGAAGATCTTCCTAGTGGGAGCTGTCTTGTCGAAGTTG

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	94.60%	4.80%	0.57%	0.00%	NA
All Indica	2759	97.30%	2.60%	0.07%	0.00%	NA
All Japonica	1512	88.50%	9.90%	1.59%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	88.40%	11.40%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.10%	0.65%	0.00%	NA
Tropical Japonica	504	68.50%	28.20%	3.37%	0.00%	NA
Japonica Intermediate	241	96.30%	2.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0529701170	C -> T	LOC_Os05g51760.1	upstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:32.058; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0529701170	C -> T	LOC_Os05g51770.1	downstream_gene_variant ; 2450.0bp to feature; MODIFIER	silent_mutation	Average:32.058; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0529701170	C -> T	LOC_Os05g51760-LOC_Os05g51770	intergenic_region ; MODIFIER	silent_mutation	Average:32.058; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529701170	6.72E-07	3.70E-07	mr1794	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