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Detailed information for vg0336117363:

Variant ID: vg0336117363 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 36117363
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTTGCACGTAAAGTTTATGTTTTTATGTATAGATTACAGAACTCAGATCTGTACTGGGTCAAACTTCTGTTTATCCCTAAGGACTGCCAGGGGGTTCAG[C/A]
TTATACAAAAGCTAATATAAAATTTCTTTTCTGAAAGTATCTCATTTCCAAAATTTGTAAAGATAAATTGCTGTAAACATGTTTATAAGTTTAATATTAA

Reverse complement sequence

TTAATATTAAACTTATAAACATGTTTACAGCAATTTATCTTTACAAATTTTGGAAATGAGATACTTTCAGAAAAGAAATTTTATATTAGCTTTTGTATAA[G/T]
CTGAACCCCCTGGCAGTCCTTAGGGATAAACAGAAGTTTGACCCAGTACAGATCTGAGTTCTGTAATCTATACATAAAAACATAAACTTTACGTGCAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	4.00%	0.21%	0.00%	NA
All Indica	2759	92.90%	6.80%	0.36%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	94.80%	4.50%	0.65%	0.00%	NA
Indica III	913	86.20%	13.40%	0.44%	0.00%	NA
Indica Intermediate	786	94.30%	5.50%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0336117363	C -> A	LOC_Os03g63930.1	downstream_gene_variant ; 2255.0bp to feature; MODIFIER	silent_mutation	Average:39.746; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0336117363	C -> A	LOC_Os03g63930.2	downstream_gene_variant ; 2808.0bp to feature; MODIFIER	silent_mutation	Average:39.746; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0336117363	C -> A	LOC_Os03g63920.1	intron_variant ; MODIFIER	silent_mutation	Average:39.746; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0336117363	2.78E-06	2.74E-08	mr1291	Ind_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
vg0336117363	4.76E-06	1.74E-07	mr1479	Ind_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
vg0336117363	NA	9.23E-06	mr1502	Ind_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
vg0336117363	NA	6.04E-06	mr1522	Ind_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
vg0336117363	NA	5.55E-06	mr1543	Ind_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
vg0336117363	3.19E-06	3.21E-07	mr1553	Ind_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
vg0336117363	NA	1.32E-06	mr1742	Ind_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
vg0336117363	4.08E-07	1.42E-08	mr1892	Ind_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
vg0336117363	2.00E-06	7.94E-08	mr1975	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