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Detailed information for vg0434702618:

Variant ID: vg0434702618 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34702618
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, C: 0.09, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTATTGGTACATTGACTTTCGCCAAGCACCCCCCATGTGCGCAAATAAGAAAGTGATGGTTTTCTCCCAATCCATATCTCATATGGTGTTTTGTCCTT[C/A]
TTTCTGTTAGGAACTCTGTTTAACACATGATTCGAGGTCAACAATGCCTCCCCCCACCATGCCTTAGGTAGTCCCGCGGTGTCTAACATGGCATTCACCA

Reverse complement sequence

TGGTGAATGCCATGTTAGACACCGCGGGACTACCTAAGGCATGGTGGGGGGAGGCATTGTTGACCTCGAATCATGTGTTAAACAGAGTTCCTAACAGAAA[G/T]
AAGGACAAAACACCATATGAGATATGGATTGGGAGAAAACCATCACTTTCTTATTTGCGCACATGGGGGGTGCTTGGCGAAAGTCAATGTACCAATAACG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.80%	32.90%	0.21%	0.00%	NA
All Indica	2759	96.00%	3.60%	0.33%	0.00%	NA
All Japonica	1512	13.20%	86.80%	0.00%	0.00%	NA
Aus	269	85.90%	14.10%	0.00%	0.00%	NA
Indica I	595	97.00%	3.00%	0.00%	0.00%	NA
Indica II	465	96.80%	2.80%	0.43%	0.00%	NA
Indica III	913	97.90%	1.60%	0.44%	0.00%	NA
Indica Intermediate	786	92.70%	6.90%	0.38%	0.00%	NA
Temperate Japonica	767	4.60%	95.40%	0.00%	0.00%	NA
Tropical Japonica	504	8.10%	91.90%	0.00%	0.00%	NA
Japonica Intermediate	241	51.00%	49.00%	0.00%	0.00%	NA
VI/Aromatic	96	35.40%	64.60%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	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
vg0434702618	C -> A	LOC_Os04g58300.1	missense_variant ; p.Lys438Asn; MODERATE	nonsynonymous_codon ; K438N	Average:24.11; most accessible tissue: Minghui63 panicle, score: 34.226	benign	-0.277	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434702618	8.03E-06	NA	mr1008	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
vg0434702618	3.04E-06	NA	mr1009	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
vg0434702618	NA	1.75E-06	mr1064	Jap_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
vg0434702618	NA	3.81E-10	mr1128	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
vg0434702618	NA	6.07E-13	mr1239	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
vg0434702618	NA	7.54E-07	mr1534	Jap_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
vg0434702618	NA	1.22E-10	mr1683	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
vg0434702618	NA	7.34E-07	mr1693	Jap_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
vg0434702618	NA	9.03E-06	mr1745	Jap_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
vg0434702618	NA	6.28E-14	mr1924	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
vg0434702618	NA	7.59E-06	mr1064_2	Jap_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
vg0434702618	NA	4.13E-44	mr1519_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
vg0434702618	NA	8.88E-07	mr1568_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
vg0434702618	NA	2.29E-11	mr1722_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
vg0434702618	NA	6.43E-06	mr1745_2	Jap_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