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Detailed information for vg0818047553:

Variant ID: vg0818047553 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18047553
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACTTAGTCCTCACCATGAAGAAAACTGCAGCGGAAAAATAAAACCTAGCGAGCTTCAGCTCCACTCCCACAGGCAGCTCAACTGGGGTATAAGCCAAA[G/C]
GTCTTCTCCTTCAGAATCCTTTTTCTTCAACTGAGGTTTGATGATTATTGCAAGGTGAGCATATGACATACTCAGCAAGCCACATAGCATATATGCAAGT

Reverse complement sequence

ACTTGCATATATGCTATGTGGCTTGCTGAGTATGTCATATGCTCACCTTGCAATAATCATCAAACCTCAGTTGAAGAAAAAGGATTCTGAAGGAGAAGAC[C/G]
TTTGGCTTATACCCCAGTTGAGCTGCCTGTGGGAGTGGAGCTGAAGCTCGCTAGGTTTTATTTTTCCGCTGCAGTTTTCTTCATGGTGAGGACTAAGTGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	22.10%	0.89%	25.54%	NA
All Indica	2759	70.20%	2.90%	1.27%	25.63%	NA
All Japonica	1512	23.30%	61.80%	0.40%	14.48%	NA
Aus	269	4.10%	2.60%	0.37%	92.94%	NA
Indica I	595	58.80%	7.70%	1.85%	31.60%	NA
Indica II	465	91.00%	0.60%	0.65%	7.74%	NA
Indica III	913	72.40%	0.90%	1.31%	25.41%	NA
Indica Intermediate	786	63.90%	3.10%	1.15%	31.93%	NA
Temperate Japonica	767	13.20%	85.30%	0.00%	1.56%	NA
Tropical Japonica	504	31.30%	31.00%	0.99%	36.71%	NA
Japonica Intermediate	241	39.00%	51.50%	0.41%	9.13%	NA
VI/Aromatic	96	86.50%	1.00%	0.00%	12.50%	NA
Intermediate	90	54.40%	24.40%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818047553	G -> C	LOC_Os08g29430.1	upstream_gene_variant ; 1209.0bp to feature; MODIFIER	silent_mutation	Average:39.0; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0818047553	G -> C	LOC_Os08g29440.1	upstream_gene_variant ; 1599.0bp to feature; MODIFIER	silent_mutation	Average:39.0; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0818047553	G -> C	LOC_Os08g29430-LOC_Os08g29440	intergenic_region ; MODIFIER	silent_mutation	Average:39.0; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0818047553	G -> DEL	N	N	silent_mutation	Average:39.0; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818047553	4.30E-06	NA	mr1301	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
vg0818047553	NA	2.98E-09	mr1368	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
vg0818047553	NA	9.05E-06	mr1368	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
vg0818047553	NA	2.49E-08	mr1439	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
vg0818047553	NA	1.73E-07	mr1584	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
vg0818047553	NA	1.26E-13	mr1853	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
vg0818047553	NA	1.33E-08	mr1986	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
vg0818047553	3.07E-06	3.07E-06	mr1474_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