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Detailed information for vg0433598971:

Variant ID: vg0433598971 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 33598971
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAGAGGGGAGGAGAAGAGGAAGGGGGGAGGGGAGGAGGAAGAGGATTGGATCTGAGAAGAGCAAGAGAGGGGATGTTCCAATCTTACCTAAATATCTG[T/C]
CTGGGACTTAACCGATCGGATGTGGGAGAGAAATATTTACTCCCGGTTGATAACTTCAACCGGGACTAAAGATCGATCTTTAGTCCCGGTTGGTAATACC

Reverse complement sequence

GGTATTACCAACCGGGACTAAAGATCGATCTTTAGTCCCGGTTGAAGTTATCAACCGGGAGTAAATATTTCTCTCCCACATCCGATCGGTTAAGTCCCAG[A/G]
CAGATATTTAGGTAAGATTGGAACATCCCCTCTCTTGCTCTTCTCAGATCCAATCCTCTTCCTCCTCCCCTCCCCCCTTCCTCTTCTCCTCCCCTCTCCT

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	93.30%	6.00%	0.66%	0.00%	NA
All Indica	2759	89.10%	9.90%	1.01%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.90%	8.10%	1.01%	0.00%	NA
Indica II	465	94.00%	5.80%	0.22%	0.00%	NA
Indica III	913	87.70%	11.80%	0.44%	0.00%	NA
Indica Intermediate	786	86.30%	11.60%	2.16%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0433598971	T -> C	LOC_Os04g56360.1	downstream_gene_variant ; 2872.0bp to feature; MODIFIER	silent_mutation	Average:27.313; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0433598971	T -> C	LOC_Os04g56360-LOC_Os04g56370	intergenic_region ; MODIFIER	silent_mutation	Average:27.313; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0433598971	2.00E-06	1.65E-07	mr1681_2	Ind_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