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Detailed information for vg0401608764:

Variant ID: vg0401608764 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1608764
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAACTTGTCCGGCAACTCACAGTTATTGTTCTCAAGTTCCTTAGCCAGCATCTGAATCTCATGAGCTTGTTCCACTACAGAACGGTCATCGACCATCTT[G/A]
TAGTCAAAGAACTGCTCCATGACATACAGCTCACTGCTGGCGTCGGAAACTCCGAACTTGGCCTCAAGTGCATCCCACATGTCCTTCCCTAAAGGCATGT

Reverse complement sequence

ACATGCCTTTAGGGAAGGACATGTGGGATGCACTTGAGGCCAAGTTCGGAGTTTCCGACGCCAGCAGTGAGCTGTATGTCATGGAGCAGTTCTTTGACTA[C/T]
AAGATGGTCGATGACCGTTCTGTAGTGGAACAAGCTCATGAGATTCAGATGCTGGCTAAGGAACTTGAGAACAATAACTGTGAGTTGCCGGACAAGTTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.10%	10.50%	29.37%	17.05%	NA
All Indica	2759	37.30%	17.50%	38.67%	6.52%	NA
All Japonica	1512	45.80%	0.50%	16.20%	37.57%	NA
Aus	269	79.90%	0.70%	17.10%	2.23%	NA
Indica I	595	54.80%	1.70%	38.49%	5.04%	NA
Indica II	465	18.30%	33.30%	41.29%	7.10%	NA
Indica III	913	36.50%	25.00%	31.87%	6.68%	NA
Indica Intermediate	786	36.30%	11.50%	45.17%	7.12%	NA
Temperate Japonica	767	62.80%	0.40%	6.91%	29.86%	NA
Tropical Japonica	504	20.40%	0.40%	30.56%	48.61%	NA
Japonica Intermediate	241	44.40%	0.80%	15.77%	39.00%	NA
VI/Aromatic	96	54.20%	0.00%	9.38%	36.46%	NA
Intermediate	90	52.20%	5.60%	23.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401608764	G -> DEL	LOC_Os04g03640.1	N	frameshift_variant	Average:18.43; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N
vg0401608764	G -> A	LOC_Os04g03640.1	synonymous_variant ; p.Tyr82Tyr; LOW	synonymous_codon	Average:18.43; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401608764	NA	1.85E-06	mr1525	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
vg0401608764	NA	1.19E-08	mr1525	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
vg0401608764	NA	1.68E-08	mr1322_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
vg0401608764	4.80E-06	2.91E-09	mr1363_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
vg0401608764	2.14E-06	3.63E-08	mr1363_2	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