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Detailed information for vg0823144076:

Variant ID: vg0823144076 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23144076
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

GATCATAGTAAGTATTATTATTCCTCTGGGCAATGGTGGCTAACAGACGAGGCAAATTATCATAAGAAGCTTCAAATGTGCCATACTTCATCTCAATATT[C/A]
TTTTGTTTGGCTCTCCAAGCCTTTGCATAGCTTATGGTGTACTTGAATTTGTTCTCGATGTGGCTAATAATTGATTTTGGTTCAAAGCCAATGTTACCAA

Reverse complement sequence

TTGGTAACATTGGCTTTGAACCAAAATCAATTATTAGCCACATCGAGAACAAATTCAAGTACACCATAAGCTATGCAAAGGCTTGGAGAGCCAAACAAAA[G/T]
AATATTGAGATGAAGTATGGCACATTTGAAGCTTCTTATGATAATTTGCCTCGTCTGTTAGCCACCATTGCCCAGAGGAATAATAATACTTACTATGATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.30%	12.20%	1.44%	0.00%	NA
All Indica	2759	77.50%	20.10%	2.39%	0.00%	NA
All Japonica	1512	99.10%	0.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	72.40%	21.00%	6.55%	0.00%	NA
Indica II	465	41.10%	55.70%	3.23%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	77.00%	21.50%	1.53%	0.00%	NA
Temperate Japonica	767	98.70%	1.20%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	85.60%	13.30%	1.11%	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
vg0823144076	C -> A	LOC_Os08g36670.1	missense_variant ; p.Lys190Asn; MODERATE	nonsynonymous_codon ; K190N	Average:24.229; most accessible tissue: Minghui63 young leaf, score: 44.63	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823144076	9.93E-07	NA	mr1699	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
vg0823144076	2.39E-07	6.53E-08	mr1699	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
vg0823144076	NA	9.45E-06	mr1727	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
vg0823144076	NA	5.43E-06	mr1469_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