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Detailed information for vg0224703299:

Variant ID: vg0224703299 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24703299
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGCGGGGTGGCTGCACGCGGGTTGGACCAATACAATCTCCTCCTCTCCTTTTTTAACTCATCTCCTCACAGAGTCACCCTTATCTCTTTCTCTCCCT[C/T]
CTCCCTTCCTCTCCTCCTCTCCCTCCTCCCCACCTCCCTCTGCAATGGCGGGGCGCATAGGCCCGGTCGGCCAGCGTGGCGGCGTGGCGCGCGGAGGGCC

Reverse complement sequence

GGCCCTCCGCGCGCCACGCCGCCACGCTGGCCGACCGGGCCTATGCGCCCCGCCATTGCAGAGGGAGGTGGGGAGGAGGGAGAGGAGGAGAGGAAGGGAG[G/A]
AGGGAGAGAAAGAGATAAGGGTGACTCTGTGAGGAGATGAGTTAAAAAAGGAGAGGAGGAGATTGTATTGGTCCAACCCGCGTGCAGCCACCCCGCTTAT

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	83.30%	14.50%	1.95%	0.28%	NA
All Indica	2759	93.10%	5.60%	1.12%	0.18%	NA
All Japonica	1512	69.20%	30.60%	0.13%	0.00%	NA
Aus	269	73.60%	1.50%	21.93%	2.97%	NA
Indica I	595	98.00%	1.30%	0.67%	0.00%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	92.60%	6.10%	1.10%	0.22%	NA
Indica Intermediate	786	88.40%	9.20%	2.04%	0.38%	NA
Temperate Japonica	767	56.10%	43.70%	0.26%	0.00%	NA
Tropical Japonica	504	87.50%	12.50%	0.00%	0.00%	NA
Japonica Intermediate	241	73.00%	27.00%	0.00%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	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
vg0224703299	C -> T	LOC_Os02g40750.1	upstream_gene_variant ; 4851.0bp to feature; MODIFIER	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0224703299	C -> T	LOC_Os02g40760.1	upstream_gene_variant ; 1621.0bp to feature; MODIFIER	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0224703299	C -> T	LOC_Os02g40770.1	upstream_gene_variant ; 4775.0bp to feature; MODIFIER	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0224703299	C -> T	LOC_Os02g40770.2	upstream_gene_variant ; 4686.0bp to feature; MODIFIER	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0224703299	C -> T	LOC_Os02g40760-LOC_Os02g40770	intergenic_region ; MODIFIER	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0224703299	C -> DEL	N	N	silent_mutation	Average:43.37; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224703299	4.49E-06	NA	mr1449	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