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Detailed information for vg0142631029:

Variant ID: vg0142631029 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42631029
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

AACTGCGACTATACCATCACAGTGTGGAGACTGATGCGGCAATGGATCAGCGCTTACTTCCCCATCCCTGGGAGCGAAAACACATGCCTGACAGAGTGGT[G/C]
GTTGCAGGCCAGAACATGTTTTCGGAAGTGCTACAGGACAAACTTCGACAGCGCTTGTATGCTGATTTGCTGGCAGATTTGGAAGGAAAGAAATGCGCGT

Reverse complement sequence

ACGCGCATTTCTTTCCTTCCAAATCTGCCAGCAAATCAGCATACAAGCGCTGTCGAAGTTTGTCCTGTAGCACTTCCGAAAACATGTTCTGGCCTGCAAC[C/G]
ACCACTCTGTCAGGCATGTGTTTTCGCTCCCAGGGATGGGGAAGTAAGCGCTGATCCATTGCCGCATCAGTCTCCACACTGTGATGGTATAGTCGCAGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.90%	10.70%	11.72%	6.62%	NA
All Indica	2759	72.30%	12.40%	9.64%	5.69%	NA
All Japonica	1512	66.90%	7.30%	16.80%	8.99%	NA
Aus	269	76.60%	16.00%	4.46%	2.97%	NA
Indica I	595	76.50%	0.50%	18.15%	4.87%	NA
Indica II	465	90.80%	6.90%	1.72%	0.65%	NA
Indica III	913	57.30%	25.00%	8.54%	9.20%	NA
Indica Intermediate	786	75.60%	10.10%	9.16%	5.22%	NA
Temperate Japonica	767	73.90%	0.30%	17.60%	8.21%	NA
Tropical Japonica	504	57.30%	20.60%	13.89%	8.13%	NA
Japonica Intermediate	241	64.30%	2.10%	20.33%	13.28%	NA
VI/Aromatic	96	77.10%	1.00%	15.62%	6.25%	NA
Intermediate	90	73.30%	12.20%	7.78%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0142631029	G -> DEL	N	N	silent_mutation	Average:63.157; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0142631029	G -> C	LOC_Os01g73580.1	downstream_gene_variant ; 589.0bp to feature; MODIFIER	silent_mutation	Average:63.157; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0142631029	G -> C	LOC_Os01g73590.1	downstream_gene_variant ; 4699.0bp to feature; MODIFIER	silent_mutation	Average:63.157; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0142631029	G -> C	LOC_Os01g73580-LOC_Os01g73590	intergenic_region ; MODIFIER	silent_mutation	Average:63.157; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142631029	NA	2.36E-06	mr1422	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
vg0142631029	NA	1.11E-09	mr1583	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
vg0142631029	8.60E-07	8.60E-07	mr1929	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
vg0142631029	NA	1.05E-07	mr1422_2	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
vg0142631029	NA	3.80E-07	mr1583_2	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
vg0142631029	2.02E-06	7.46E-14	mr1850_2	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