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Detailed information for vg0401600042:

Variant ID: vg0401600042 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1600042
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCATCCTGATGAGATCTTCAGCATTTCTACCCAACTTCCTGAATGTAGTATAAGGCATCAAATTTACTGCAGCCCCACCATCAACCATCATCTTAGACA[T/A]
CGGCTTCCCATTGACATAGCCATTTATATACAATGGTTTAAGGTCCCGATTCTCCGTCCCCTCAGGCTTTTCAAAGACTGCTTGTTCTAGCGATAGGACC

Reverse complement sequence

GGTCCTATCGCTAGAACAAGCAGTCTTTGAAAAGCCTGAGGGGACGGAGAATCGGGACCTTAAACCATTGTATATAAATGGCTATGTCAATGGGAAGCCG[A/T]
TGTCTAAGATGATGGTTGATGGTGGGGCTGCAGTAAATTTGATGCCTTATACTACATTCAGGAAGTTGGGTAGAAATGCTGAAGATCTCATCAGGATGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.60%	1.70%	4.27%	4.44%	NA
All Indica	2759	92.60%	2.10%	5.18%	0.14%	NA
All Japonica	1512	85.40%	0.00%	1.32%	13.29%	NA
Aus	269	84.00%	5.90%	9.67%	0.37%	NA
Indica I	595	93.10%	1.30%	5.55%	0.00%	NA
Indica II	465	98.90%	0.40%	0.65%	0.00%	NA
Indica III	913	88.90%	3.10%	7.56%	0.44%	NA
Indica Intermediate	786	92.60%	2.50%	4.83%	0.00%	NA
Temperate Japonica	767	77.60%	0.00%	1.69%	20.73%	NA
Tropical Japonica	504	98.20%	0.00%	0.20%	1.59%	NA
Japonica Intermediate	241	83.40%	0.00%	2.49%	14.11%	NA
VI/Aromatic	96	88.50%	4.20%	6.25%	1.04%	NA
Intermediate	90	87.80%	1.10%	7.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401600042	T -> DEL	LOC_Os04g03630.1	N	frameshift_variant	Average:28.409; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N
vg0401600042	T -> A	LOC_Os04g03630.1	missense_variant ; p.Met983Leu; MODERATE	nonsynonymous_codon ; M983L	Average:28.409; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	benign	0.051	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401600042	1.89E-06	NA	mr1946	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
vg0401600042	2.70E-06	1.91E-06	mr1946	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