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Detailed information for vg0412131185:

Variant ID: vg0412131185 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12131185
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGGGAGTTCCATGCGCTTCATTAGGGAAACAAGATAGCTATAGAGTACCTACACGAGTTCAACCGCCTATTATTATTTATTACGACGACAGAATAATC[C/T]
GCAAGCGCACAAATACAGTCGTAGCCTTCACCCCAAGAGTATTCCAGGATATAGTATCCACAGGCAACGTATGTGTATAATCTAAGAACGAGATTCTTCC

Reverse complement sequence

GGAAGAATCTCGTTCTTAGATTATACACATACGTTGCCTGTGGATACTATATCCTGGAATACTCTTGGGGTGAAGGCTACGACTGTATTTGTGCGCTTGC[G/A]
GATTATTCTGTCGTCGTAATAAATAATAATAGGCGGTTGAACTCGTGTAGGTACTCTATAGCTATCTTGTTTCCCTAATGAAGCGCATGGAACTCCCTCT

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	81.20%	17.80%	0.36%	0.68%	NA
All Indica	2759	98.40%	0.50%	0.25%	0.87%	NA
All Japonica	1512	51.20%	47.90%	0.60%	0.26%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.10%	1.30%	0.00%	0.65%	NA
Indica III	913	97.60%	0.20%	0.55%	1.64%	NA
Indica Intermediate	786	98.50%	0.50%	0.25%	0.76%	NA
Temperate Japonica	767	86.70%	12.40%	0.91%	0.00%	NA
Tropical Japonica	504	4.20%	94.80%	0.40%	0.60%	NA
Japonica Intermediate	241	36.50%	63.10%	0.00%	0.41%	NA
VI/Aromatic	96	15.60%	83.30%	0.00%	1.04%	NA
Intermediate	90	71.10%	24.40%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412131185	C -> DEL	N	N	silent_mutation	Average:55.887; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg0412131185	C -> T	LOC_Os04g21450.1	upstream_gene_variant ; 2862.0bp to feature; MODIFIER	silent_mutation	Average:55.887; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg0412131185	C -> T	LOC_Os04g21450-LOC_Os04g21460	intergenic_region ; MODIFIER	silent_mutation	Average:55.887; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412131185	NA	1.43E-11	mr1552	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
vg0412131185	NA	6.95E-10	mr1905	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
vg0412131185	NA	2.81E-06	mr1964	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
vg0412131185	NA	8.96E-10	mr1993	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
vg0412131185	NA	2.59E-09	mr1851_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
vg0412131185	NA	1.71E-13	mr1864_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