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Detailed information for vg0522745440:

Variant ID: vg0522745440 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22745440
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCATTTGACAAAGTTTCCCTTATTATTGCTCCTCTGCATCTTCTTCCTCCTCTTCCTCCCCTTCCTCTTCTTCGTTGTCGTTGTCGTCGTCGTCGTC[G/T]
TCCGAGGAAGACGACGACGAGCTATCAGAGTGATCTGATTTTGGTGCAGGGGAGGCAGATGGAGCTGGGGCTGGGACGCTGGCAGCTGGTGGATCCGGTG

Reverse complement sequence

CACCGGATCCACCAGCTGCCAGCGTCCCAGCCCCAGCTCCATCTGCCTCCCCTGCACCAAAATCAGATCACTCTGATAGCTCGTCGTCGTCTTCCTCGGA[C/A]
GACGACGACGACGACAACGACAACGAAGAAGAGGAAGGGGAGGAAGAGGAGGAAGAAGATGCAGAGGAGCAATAATAAGGGAAACTTTGTCAAATGATAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.30%	4.70%	0.00%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.00%	0.00%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	92.90%	7.10%	0.00%	0.00%	NA
Indica III	913	88.80%	11.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	92.10%	7.90%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0522745440	G -> T	LOC_Os05g38770.1	missense_variant ; p.Asp393Glu; MODERATE	nonsynonymous_codon ; D393E	Average:48.236; most accessible tissue: Zhenshan97 young leaf, score: 80.056	unknown	unknown	TOLERATED	0.47

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522745440	NA	7.77E-06	mr1671	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