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Detailed information for vg1126180021:

Variant ID: vg1126180021 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26180021
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.41, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGCATGGACATGTTGTTTATGAATTTCTGGACTGAAGCATCCAGAACGCAGTGTTTACACCCAAATTTGGCACTTAGGATTAAAATAGGAAATATTGC[T/C]
AAAATTTGGAAGTCTACCGGTTTCCTCCGAGGTAGGCCGGTCTGACCGCCGTGTGTTGGGCGGTCAGACCGCCGGTTGAGGGCCGGTCAGACCGGCGGTG

Reverse complement sequence

CACCGCCGGTCTGACCGGCCCTCAACCGGCGGTCTGACCGCCCAACACACGGCGGTCAGACCGGCCTACCTCGGAGGAAACCGGTAGACTTCCAAATTTT[A/G]
GCAATATTTCCTATTTTAATCCTAAGTGCCAAATTTGGGTGTAAACACTGCGTTCTGGATGCTTCAGTCCAGAAATTCATAAACAACATGTCCATGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.00%	25.80%	1.25%	42.98%	NA
All Indica	2759	13.80%	27.10%	1.67%	57.41%	NA
All Japonica	1512	65.30%	20.00%	0.33%	14.35%	NA
Aus	269	2.20%	42.00%	1.49%	54.28%	NA
Indica I	595	7.90%	21.30%	1.85%	68.91%	NA
Indica II	465	7.50%	62.40%	2.15%	27.96%	NA
Indica III	913	22.30%	8.00%	1.20%	68.46%	NA
Indica Intermediate	786	12.00%	33.00%	1.78%	53.31%	NA
Temperate Japonica	767	64.40%	32.50%	0.39%	2.74%	NA
Tropical Japonica	504	71.40%	3.40%	0.40%	24.80%	NA
Japonica Intermediate	241	55.20%	15.40%	0.00%	29.46%	NA
VI/Aromatic	96	18.80%	31.20%	2.08%	47.92%	NA
Intermediate	90	30.00%	25.60%	2.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126180021	T -> DEL	N	N	silent_mutation	Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg1126180021	T -> C	LOC_Os11g43370.1	upstream_gene_variant ; 1405.0bp to feature; MODIFIER	silent_mutation	Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg1126180021	T -> C	LOC_Os11g43360-LOC_Os11g43370	intergenic_region ; MODIFIER	silent_mutation	Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126180021	6.76E-06	9.35E-08	mr1668	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
vg1126180021	NA	8.29E-06	mr1060_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
vg1126180021	NA	9.69E-06	mr1358_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
vg1126180021	NA	1.39E-06	mr1576_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