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Detailed information for vg0417549349:

Variant ID: vg0417549349 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17549349
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAAGATGGGTTTTGTAGAAAAACAGCTAAACCAGCTAAACCAGCTAGTAGAGCCGATTTAGAGAACAAAATCAGCCTCTAGGCCGATTTAGATCGATA[T/C]
GAGGATAACTACCCGTCTCGTGGGCAAAACGGAAGGTTTTCAAGACAAACCTACAAAGAGGTGTTGCACTCTCACAGCGGCGGCGGACTGTTTACGGCGC

Reverse complement sequence

GCGCCGTAAACAGTCCGCCGCCGCTGTGAGAGTGCAACACCTCTTTGTAGGTTTGTCTTGAAAACCTTCCGTTTTGCCCACGAGACGGGTAGTTATCCTC[A/G]
TATCGATCTAAATCGGCCTAGAGGCTGATTTTGTTCTCTAAATCGGCTCTACTAGCTGGTTTAGCTGGTTTAGCTGTTTTTCTACAAAACCCATCTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.20%	0.10%	0.13%	13.58%	NA
All Indica	2759	85.80%	0.10%	0.14%	13.95%	NA
All Japonica	1512	86.30%	0.00%	0.13%	13.56%	NA
Aus	269	83.30%	0.40%	0.00%	16.36%	NA
Indica I	595	91.10%	0.00%	0.50%	8.40%	NA
Indica II	465	84.10%	0.00%	0.00%	15.91%	NA
Indica III	913	82.10%	0.20%	0.11%	17.52%	NA
Indica Intermediate	786	87.00%	0.10%	0.00%	12.85%	NA
Temperate Japonica	767	76.80%	0.00%	0.26%	22.95%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	88.80%	0.00%	0.00%	11.20%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	92.20%	0.00%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417549349	T -> C	LOC_Os04g29530.1	upstream_gene_variant ; 3493.0bp to feature; MODIFIER	silent_mutation	Average:22.802; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0417549349	T -> C	LOC_Os04g29530-LOC_Os04g29540	intergenic_region ; MODIFIER	silent_mutation	Average:22.802; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0417549349	T -> DEL	N	N	silent_mutation	Average:22.802; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417549349	3.59E-06	4.56E-06	mr1071_2	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
vg0417549349	9.24E-07	6.14E-06	mr1203_2	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
vg0417549349	2.73E-06	NA	mr1613_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
vg0417549349	2.89E-06	4.51E-06	mr1913_2	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