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Detailed information for vg1120972390:

Variant ID: vg1120972390 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20972390
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAAGTTCTTCTTCTGTTCTTCATCATCCCCTCCCTCTTCTCACTTTTTCTGGATTAAAAAAAAAATCATGGAGAACTCGCCTAGTGAATTTGGTGGTG[G/T]
TTTCCCAACCTCCATCATTCCCTTGTTTTCCTTTTTTTTAGAAATGTTCTATAGAAAAAGTTACGGTAAAAAACCATATTAACTCATTTTTCAAGTTTTT

Reverse complement sequence

AAAAACTTGAAAAATGAGTTAATATGGTTTTTTACCGTAACTTTTTCTATAGAACATTTCTAAAAAAAAGGAAAACAAGGGAATGATGGAGGTTGGGAAA[C/A]
CACCACCAAATTCACTAGGCGAGTTCTCCATGATTTTTTTTTTAATCCAGAAAAAGTGAGAAGAGGGAGGGGATGATGAAGAACAGAAGAAGAACTTGGA

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	62.50%	35.60%	0.02%	1.82%	NA
All Indica	2759	91.30%	7.40%	0.00%	1.30%	NA
All Japonica	1512	9.70%	87.20%	0.07%	3.11%	NA
Aus	269	82.90%	16.70%	0.00%	0.37%	NA
Indica I	595	81.70%	18.30%	0.00%	0.00%	NA
Indica II	465	95.70%	1.50%	0.00%	2.80%	NA
Indica III	913	92.90%	6.00%	0.00%	1.10%	NA
Indica Intermediate	786	94.10%	4.20%	0.00%	1.65%	NA
Temperate Japonica	767	7.40%	92.30%	0.13%	0.13%	NA
Tropical Japonica	504	13.10%	77.80%	0.00%	9.13%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	54.40%	43.30%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120972390	G -> T	LOC_Os11g35730.1	upstream_gene_variant ; 2196.0bp to feature; MODIFIER	silent_mutation	Average:61.018; most accessible tissue: Minghui63 root, score: 78.594	N	N	N	N
vg1120972390	G -> T	LOC_Os11g35720-LOC_Os11g35730	intergenic_region ; MODIFIER	silent_mutation	Average:61.018; most accessible tissue: Minghui63 root, score: 78.594	N	N	N	N
vg1120972390	G -> DEL	N	N	silent_mutation	Average:61.018; most accessible tissue: Minghui63 root, score: 78.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120972390	NA	8.44E-06	mr1060	Ind_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
vg1120972390	9.95E-06	1.45E-06	mr1511	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
vg1120972390	NA	5.54E-14	mr1035_2	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
vg1120972390	3.73E-06	6.46E-06	mr1211_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
vg1120972390	1.13E-06	1.13E-06	mr1527_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