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Detailed information for vg0431372747:

Variant ID: vg0431372747 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31372747
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGCCTCCAATAATCTAAAGAAACAAACAATTCATAGCTTATTCTATGTCAGCTTATTATAATCCAGCTTAGAGTAATATGATTTAATAATCTAGATTA[C/T]
AATAATCTTAAGCGGAAACAAACAGGGCCTTACATTGTGAAACGGAGGAAGTACACACTTAGGAGAAAAATCACGAGACGAATCTTTTTAGCATAATTAG

Reverse complement sequence

CTAATTATGCTAAAAAGATTCGTCTCGTGATTTTTCTCCTAAGTGTGTACTTCCTCCGTTTCACAATGTAAGGCCCTGTTTGTTTCCGCTTAAGATTATT[G/A]
TAATCTAGATTATTAAATCATATTACTCTAAGCTGGATTATAATAAGCTGACATAGAATAAGCTATGAATTGTTTGTTTCTTTAGATTATTGGAGGCATC

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	91.40%	7.90%	0.70%	0.00%	NA
All Indica	2759	94.00%	5.50%	0.51%	0.00%	NA
All Japonica	1512	89.00%	10.00%	1.06%	0.00%	NA
Aus	269	92.90%	5.90%	1.12%	0.00%	NA
Indica I	595	97.50%	1.70%	0.84%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	90.70%	9.20%	0.11%	0.00%	NA
Indica Intermediate	786	91.70%	7.30%	1.02%	0.00%	NA
Temperate Japonica	767	91.70%	6.80%	1.56%	0.00%	NA
Tropical Japonica	504	95.60%	4.40%	0.00%	0.00%	NA
Japonica Intermediate	241	66.40%	32.00%	1.66%	0.00%	NA
VI/Aromatic	96	47.90%	52.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0431372747	C -> T	LOC_Os04g52690.1	upstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:45.756; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0431372747	C -> T	LOC_Os04g52690.2	upstream_gene_variant ; 3348.0bp to feature; MODIFIER	silent_mutation	Average:45.756; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0431372747	C -> T	LOC_Os04g52690.3	upstream_gene_variant ; 3348.0bp to feature; MODIFIER	silent_mutation	Average:45.756; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0431372747	C -> T	LOC_Os04g52690-LOC_Os04g52700	intergenic_region ; MODIFIER	silent_mutation	Average:45.756; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431372747	9.31E-06	9.31E-06	mr1426	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
vg0431372747	4.85E-06	4.85E-06	mr1915	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