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Detailed information for vg1121882641:

Variant ID: vg1121882641 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21882641
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAGGTTGACTTGGTAGCGAGAATGCTCGTGGAAGCATGCGACTTGGGTGAGAATGTGCTGATTCTTGGGCACAACCAATCGCTTTGTCTCCGTGCTGA[T/A]
GAATATCCTCTGCTGAAGGCGAATCATGTCTACTTCAGTGATGATAGAGAGCTCTATATTAAAGGATGCAAGAATGGCTGCCGTGATATTGGAGTGTTCA

Reverse complement sequence

TGAACACTCCAATATCACGGCAGCCATTCTTGCATCCTTTAATATAGAGCTCTCTATCATCACTGAAGTAGACATGATTCGCCTTCAGCAGAGGATATTC[A/T]
TCAGCACGGAGACAAAGCGATTGGTTGTGCCCAAGAATCAGCACATTCTCACCCAAGTCGCATGCTTCCACGAGCATTCTCGCTACCAAGTCAACCTTGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.10%	27.70%	0.21%	0.00%	NA
All Indica	2759	93.90%	5.90%	0.22%	0.00%	NA
All Japonica	1512	32.50%	67.50%	0.07%	0.00%	NA
Aus	269	89.20%	10.80%	0.00%	0.00%	NA
Indica I	595	96.10%	3.90%	0.00%	0.00%	NA
Indica II	465	97.40%	2.20%	0.43%	0.00%	NA
Indica III	913	93.80%	5.90%	0.33%	0.00%	NA
Indica Intermediate	786	90.20%	9.70%	0.13%	0.00%	NA
Temperate Japonica	767	16.30%	83.70%	0.00%	0.00%	NA
Tropical Japonica	504	62.90%	36.90%	0.20%	0.00%	NA
Japonica Intermediate	241	20.30%	79.70%	0.00%	0.00%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	63.30%	33.30%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121882641	T -> A	LOC_Os11g37060.1	missense_variant ; p.Asp342Glu; MODERATE	nonsynonymous_codon ; D342E	Average:20.167; most accessible tissue: Zhenshan97 root, score: 38.035	benign	0.266	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121882641	NA	1.25E-06	mr1629	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
vg1121882641	7.60E-06	2.85E-20	mr1679	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
vg1121882641	NA	2.93E-08	mr1691	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
vg1121882641	NA	3.80E-09	mr1693	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
vg1121882641	NA	8.22E-08	mr1780	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
vg1121882641	7.86E-08	9.82E-26	mr1679_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
vg1121882641	NA	3.61E-07	mr1679_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
vg1121882641	NA	7.91E-08	mr1691_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
vg1121882641	1.61E-06	1.61E-06	mr1760_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