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Detailed information for vg1126137805:

Variant ID: vg1126137805 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26137805
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, C: 0.16, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

ACCCACATGTCAGCCCCTCTCCTATCTTTTTCTCCCTCTCCCCTCCTCTGCCTCTATCAAATAGTCTAACCCTGTCCTTTTTCTCCTCAGCTCACAAGGA[C/G]
CTCACCTTTGCGACGAAGAAGCGACCCCGCCACCGCTTGTCCCCCTCTTCGACGAGTTTCCTCCCTAGGCGGCGGTGTCCAGATCGGCCCCTCAGCAGAC

Reverse complement sequence

GTCTGCTGAGGGGCCGATCTGGACACCGCCGCCTAGGGAGGAAACTCGTCGAAGAGGGGGACAAGCGGTGGCGGGGTCGCTTCTTCGTCGCAAAGGTGAG[G/C]
TCCTTGTGAGCTGAGGAGAAAAAGGACAGGGTTAGACTATTTGATAGAGGCAGAGGAGGGGAGAGGGAGAAAAAGATAGGAGAGGGGCTGACATGTGGGT

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	23.70%	20.90%	0.13%	55.25%	NA
All Indica	2759	5.90%	17.40%	0.18%	76.48%	NA
All Japonica	1512	60.40%	24.90%	0.07%	14.68%	NA
Aus	269	1.90%	40.50%	0.00%	57.62%	NA
Indica I	595	6.10%	18.30%	0.17%	75.46%	NA
Indica II	465	6.00%	24.70%	0.22%	69.03%	NA
Indica III	913	3.80%	10.40%	0.11%	85.65%	NA
Indica Intermediate	786	8.10%	20.60%	0.25%	70.99%	NA
Temperate Japonica	767	85.30%	11.70%	0.13%	2.87%	NA
Tropical Japonica	504	24.00%	51.00%	0.00%	25.00%	NA
Japonica Intermediate	241	57.30%	12.00%	0.00%	30.71%	NA
VI/Aromatic	96	15.60%	5.20%	0.00%	79.17%	NA
Intermediate	90	26.70%	20.00%	0.00%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126137805	C -> DEL	N	N	silent_mutation	Average:49.381; most accessible tissue: Minghui63 root, score: 81.325	N	N	N	N
vg1126137805	C -> G	LOC_Os11g43310.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:49.381; most accessible tissue: Minghui63 root, score: 81.325	N	N	N	N
vg1126137805	C -> G	LOC_Os11g43320.1	upstream_gene_variant ; 2152.0bp to feature; MODIFIER	silent_mutation	Average:49.381; most accessible tissue: Minghui63 root, score: 81.325	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126137805	NA	2.08E-06	mr1808	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
vg1126137805	1.56E-06	NA	mr1806_2	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