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Detailed information for vg1126179996:

Variant ID: vg1126179996 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26179996
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

GACTGGTGAGCAGTGGATGGAATGGAAGGCATGGACATGTTGTTTATGAATTTCTGGACTGAAGCATCCAGAACGCAGTGTTTACACCCAAATTTGGCAC[T/C]
TAGGATTAAAATAGGAAATATTGCTAAAATTTGGAAGTCTACCGGTTTCCTCCGAGGTAGGCCGGTCTGACCGCCGTGTGTTGGGCGGTCAGACCGCCGG

Reverse complement sequence

CCGGCGGTCTGACCGCCCAACACACGGCGGTCAGACCGGCCTACCTCGGAGGAAACCGGTAGACTTCCAAATTTTAGCAATATTTCCTATTTTAATCCTA[A/G]
GTGCCAAATTTGGGTGTAAACACTGCGTTCTGGATGCTTCAGTCCAGAAATTCATAAACAACATGTCCATGCCTTCCATTCCATCCACTGCTCACCAGTC

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	34.30%	20.90%	0.76%	44.01%	NA
All Indica	2759	19.10%	21.00%	1.05%	58.83%	NA
All Japonica	1512	65.70%	19.50%	0.33%	14.48%	NA
Aus	269	19.00%	24.90%	0.00%	56.13%	NA
Indica I	595	21.00%	6.20%	1.85%	70.92%	NA
Indica II	465	8.20%	60.90%	1.94%	29.03%	NA
Indica III	913	22.90%	7.10%	0.55%	69.44%	NA
Indica Intermediate	786	19.80%	24.70%	0.51%	54.96%	NA
Temperate Japonica	767	64.50%	32.20%	0.52%	2.74%	NA
Tropical Japonica	504	72.40%	2.20%	0.20%	25.20%	NA
Japonica Intermediate	241	55.20%	15.40%	0.00%	29.46%	NA
VI/Aromatic	96	19.80%	31.20%	0.00%	48.96%	NA
Intermediate	90	34.40%	18.90%	2.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126179996	T -> DEL	N	N	silent_mutation	Average:49.566; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1126179996	T -> C	LOC_Os11g43370.1	upstream_gene_variant ; 1430.0bp to feature; MODIFIER	silent_mutation	Average:49.566; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1126179996	T -> C	LOC_Os11g43360-LOC_Os11g43370	intergenic_region ; MODIFIER	silent_mutation	Average:49.566; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126179996	NA	2.25E-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
vg1126179996	4.69E-06	1.24E-17	mr1715_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