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Detailed information for vg0432877331:

Variant ID: vg0432877331 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32877331
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGTCTTGTTCGGAAGCTGATTGAGAAAATATGCAGGCACAAATTGGATGCGTAAACCTTGGACTCATCAAAGCTATGCTATGGCTATGTACTAGTTGA[T/C]
GAGCTTGCCTCCAGTACTTGATAGAAGCCCATGACTCTCTATCTGAAAGTGGTCTTGGCCGTAAGCCAATAGGCGTAGTTGTAGCGAAGCGGCGTATATC

Reverse complement sequence

GATATACGCCGCTTCGCTACAACTACGCCTATTGGCTTACGGCCAAGACCACTTTCAGATAGAGAGTCATGGGCTTCTATCAAGTACTGGAGGCAAGCTC[A/G]
TCAACTAGTACATAGCCATAGCATAGCTTTGATGAGTCCAAGGTTTACGCATCCAATTTGTGCCTGCATATTTTCTCAATCAGCTTCCGAACAAGACGAC

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	66.20%	31.70%	2.16%	0.00%	NA
All Indica	2759	92.70%	4.70%	2.57%	0.00%	NA
All Japonica	1512	21.50%	77.40%	1.06%	0.00%	NA
Aus	269	51.30%	45.70%	2.97%	0.00%	NA
Indica I	595	90.30%	7.10%	2.69%	0.00%	NA
Indica II	465	93.80%	3.20%	3.01%	0.00%	NA
Indica III	913	93.80%	3.60%	2.63%	0.00%	NA
Indica Intermediate	786	92.70%	5.10%	2.16%	0.00%	NA
Temperate Japonica	767	6.50%	92.40%	1.04%	0.00%	NA
Tropical Japonica	504	37.50%	61.30%	1.19%	0.00%	NA
Japonica Intermediate	241	35.70%	63.50%	0.83%	0.00%	NA
VI/Aromatic	96	58.30%	36.50%	5.21%	0.00%	NA
Intermediate	90	55.60%	42.20%	2.22%	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
vg0432877331	T -> C	LOC_Os04g55300.1	downstream_gene_variant ; 2937.0bp to feature; MODIFIER	silent_mutation	Average:19.632; most accessible tissue: Callus, score: 27.594	N	N	N	N
vg0432877331	T -> C	LOC_Os04g55300-LOC_Os04g55310	intergenic_region ; MODIFIER	silent_mutation	Average:19.632; most accessible tissue: Callus, score: 27.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432877331	NA	2.07E-07	mr1040	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
vg0432877331	3.63E-06	3.91E-08	mr1072_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
vg0432877331	NA	1.60E-06	mr1075_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
vg0432877331	NA	7.21E-07	mr1077_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
vg0432877331	NA	5.52E-06	mr1124_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
vg0432877331	NA	1.19E-06	mr1568_2	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