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Detailed information for vg1122793429:

Variant ID: vg1122793429 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22793429
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCACTATCGGGCGTTAACGATTTCGTCACTAACGTTGGTCTCTCACCACTGAGTCATCGTGCCGTTGTCACTATCGTGCGTTGGTTTTAAGATTTCATC[T/G]
TGATTTCGCACTGTCGAACCACGATATACTATTGTCCCACAAAGATAGAGCGAGACCACACGAAGAGTGTGTGACATCACGCGATCTCGCACGGCGAGGG

Reverse complement sequence

CCCTCGCCGTGCGAGATCGCGTGATGTCACACACTCTTCGTGTGGTCTCGCTCTATCTTTGTGGGACAATAGTATATCGTGGTTCGACAGTGCGAAATCA[A/C]
GATGAAATCTTAAAACCAACGCACGATAGTGACAACGGCACGATGACTCAGTGGTGAGAGACCAACGTTAGTGACGAAATCGTTAACGCCCGATAGTGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.60%	6.70%	0.47%	53.26%	NA
All Indica	2759	40.90%	2.60%	0.54%	55.93%	NA
All Japonica	1512	42.90%	15.30%	0.33%	41.47%	NA
Aus	269	15.60%	0.00%	0.37%	84.01%	NA
Indica I	595	18.80%	0.20%	0.34%	80.67%	NA
Indica II	465	63.90%	1.50%	0.43%	34.19%	NA
Indica III	913	35.60%	5.40%	0.44%	58.60%	NA
Indica Intermediate	786	50.10%	2.00%	0.89%	46.95%	NA
Temperate Japonica	767	47.80%	19.70%	0.39%	32.07%	NA
Tropical Japonica	504	47.40%	12.90%	0.20%	39.48%	NA
Japonica Intermediate	241	17.80%	6.20%	0.41%	75.52%	NA
VI/Aromatic	96	2.10%	5.20%	0.00%	92.71%	NA
Intermediate	90	54.40%	8.90%	1.11%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122793429	T -> DEL	N	N	silent_mutation	Average:46.782; most accessible tissue: Minghui63 young leaf, score: 81.195	N	N	N	N
vg1122793429	T -> G	LOC_Os11g38470.1	downstream_gene_variant ; 1565.0bp to feature; MODIFIER	silent_mutation	Average:46.782; most accessible tissue: Minghui63 young leaf, score: 81.195	N	N	N	N
vg1122793429	T -> G	LOC_Os11g38462-LOC_Os11g38470	intergenic_region ; MODIFIER	silent_mutation	Average:46.782; most accessible tissue: Minghui63 young leaf, score: 81.195	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122793429	NA	4.02E-06	mr1807	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