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Detailed information for vg0432523918:

Variant ID: vg0432523918 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32523918
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GCGCTCGCTCCTCCAGCTCCTGGGCCCGCCCCGTCTGTTCTTCGCCGCACGTTTTTTGCTCGCGCTGGTTTCGATCGAGGACTTCGATCCACCGACGGAT[T/C]
GTGGCTTCAAGCTCCTGTGCGGAGCGAGCACGGTCATCCAAGGCCTTGCGCTCAGCCCCGAGCGCCGTCGTTCGAGCCTGCAGAGAGGCCTCAGCCTCCG

Reverse complement sequence

CGGAGGCTGAGGCCTCTCTGCAGGCTCGAACGACGGCGCTCGGGGCTGAGCGCAAGGCCTTGGATGACCGTGCTCGCTCCGCACAGGAGCTTGAAGCCAC[A/G]
ATCCGTCGGTGGATCGAAGTCCTCGATCGAAACCAGCGCGAGCAAAAAACGTGCGGCGAAGAACAGACGGGGCGGGCCCAGGAGCTGGAGGAGCGAGCGC

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	66.70%	32.80%	0.40%	0.13%	NA
All Indica	2759	73.10%	26.40%	0.33%	0.22%	NA
All Japonica	1512	64.50%	35.00%	0.53%	0.00%	NA
Aus	269	14.90%	85.10%	0.00%	0.00%	NA
Indica I	595	91.80%	8.20%	0.00%	0.00%	NA
Indica II	465	74.00%	25.80%	0.22%	0.00%	NA
Indica III	913	56.60%	42.30%	0.66%	0.44%	NA
Indica Intermediate	786	77.50%	22.00%	0.25%	0.25%	NA
Temperate Japonica	767	72.80%	26.30%	0.91%	0.00%	NA
Tropical Japonica	504	67.30%	32.70%	0.00%	0.00%	NA
Japonica Intermediate	241	32.40%	67.20%	0.41%	0.00%	NA
VI/Aromatic	96	63.50%	34.40%	2.08%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg0432523918	T -> C	LOC_Os04g54670.1	synonymous_variant ; p.Thr1459Thr; LOW	synonymous_codon	Average:70.549; most accessible tissue: Minghui63 young leaf, score: 84.596	N	N	N	N
vg0432523918	T -> DEL	LOC_Os04g54670.1	N	frameshift_variant	Average:70.549; most accessible tissue: Minghui63 young leaf, score: 84.596	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432523918	NA	4.36E-06	mr1403	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
vg0432523918	9.12E-08	9.46E-11	mr1800	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
vg0432523918	2.85E-07	5.41E-09	mr1800	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
vg0432523918	NA	2.13E-06	mr1638_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
vg0432523918	NA	9.82E-06	mr1729_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
vg0432523918	1.20E-06	1.14E-09	mr1740_2	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
vg0432523918	6.36E-09	4.81E-12	mr1741_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
vg0432523918	2.11E-08	NA	mr1771_2	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
vg0432523918	4.62E-07	NA	mr1771_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
vg0432523918	3.94E-09	NA	mr1784_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
vg0432523918	3.61E-08	6.67E-08	mr1785_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
vg0432523918	4.86E-06	1.51E-06	mr1786_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
vg0432523918	3.77E-16	1.22E-19	mr1800_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
vg0432523918	1.69E-11	2.48E-12	mr1800_2	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
vg0432523918	2.56E-07	NA	mr1873_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