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Detailed information for vg0408658440:

Variant ID: vg0408658440 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8658440
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGTGATGAAATCCATCCCAATTTCATCCCATTTCCATTCTGGTACTTGGAGAGGTTGGAGAAGTCCGGCCGGTCGTTGGTGCTTTGCTTTGACACGCT[G/A]
GCACACATCACAAAGGGCCACGAACTCTGCAATTTCCCGCTTCATACTAACCCACCAGTATTTCTCTTTCAAGTCTAAGTACATCTTCGTGCTGCCAGGG

Reverse complement sequence

CCCTGGCAGCACGAAGATGTACTTAGACTTGAAAGAGAAATACTGGTGGGTTAGTATGAAGCGGGAAATTGCAGAGTTCGTGGCCCTTTGTGATGTGTGC[C/T]
AGCGTGTCAAAGCAAAGCACCAACGACCGGCCGGACTTCTCCAACCTCTCCAAGTACCAGAATGGAAATGGGATGAAATTGGGATGGATTTCATCACCGG

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	44.10%	41.00%	14.73%	0.23%	NA
All Indica	2759	13.70%	66.00%	19.97%	0.29%	NA
All Japonica	1512	99.30%	0.40%	0.33%	0.00%	NA
Aus	269	21.20%	34.20%	44.24%	0.37%	NA
Indica I	595	6.40%	76.10%	17.14%	0.34%	NA
Indica II	465	11.60%	68.60%	19.14%	0.65%	NA
Indica III	913	17.70%	63.20%	19.06%	0.00%	NA
Indica Intermediate	786	15.90%	60.10%	23.66%	0.38%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	91.70%	1.00%	7.29%	0.00%	NA
Intermediate	90	63.30%	18.90%	15.56%	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
vg0408658440	G -> DEL	LOC_Os04g15944.1	N	frameshift_variant	Average:12.256; most accessible tissue: Callus, score: 24.786	N	N	N	N
vg0408658440	G -> A	LOC_Os04g15944.1	stop_gained ; p.Gln1116*; HIGH	stop_gained	Average:12.256; most accessible tissue: Callus, score: 24.786	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408658440	6.21E-07	NA	mr1167_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
vg0408658440	3.02E-06	NA	mr1167_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