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Detailed information for vg0408367682:

Variant ID: vg0408367682 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8367682
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAACTCGCGCTTTCATCCCTTGAAGTACCATGCCATTGGCACGTTCAACTTGTCCATTACTCATGGGATGCGCTACGGAGGCGTAACAAATCTTGATG[C/T]
CGAAGTCTTCACAAAAGTCTTTAAATACTCCGCCAGTAAATTGAGTGCCATTATCAGTAATGATCCGATTGGGTACCCCGAACCGGTGCACAATGTTGAT

Reverse complement sequence

ATCAACATTGTGCACCGGTTCGGGGTACCCAATCGGATCATTACTGATAATGGCACTCAATTTACTGGCGGAGTATTTAAAGACTTTTGTGAAGACTTCG[G/A]
CATCAAGATTTGTTACGCCTCCGTAGCGCATCCCATGAGTAATGGACAAGTTGAACGTGCCAATGGCATGGTACTTCAAGGGATGAAAGCGCGAGTTTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.20%	9.10%	26.51%	15.19%	NA
All Indica	2759	31.10%	15.00%	35.23%	18.67%	NA
All Japonica	1512	86.60%	0.30%	5.42%	7.74%	NA
Aus	269	31.60%	1.10%	43.12%	24.16%	NA
Indica I	595	26.20%	19.30%	43.36%	11.09%	NA
Indica II	465	27.50%	14.80%	42.80%	14.84%	NA
Indica III	913	33.20%	14.20%	26.51%	26.07%	NA
Indica Intermediate	786	34.40%	12.80%	34.73%	18.07%	NA
Temperate Japonica	767	97.00%	0.10%	0.91%	1.96%	NA
Tropical Japonica	504	69.40%	0.40%	13.29%	16.87%	NA
Japonica Intermediate	241	89.20%	0.40%	3.32%	7.05%	NA
VI/Aromatic	96	28.10%	0.00%	62.50%	9.38%	NA
Intermediate	90	52.20%	8.90%	25.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408367682	C -> DEL	LOC_Os04g14880.1	N	frameshift_variant	Average:11.968; most accessible tissue: Callus, score: 30.963	N	N	N	N
vg0408367682	C -> T	LOC_Os04g14880.1	missense_variant ; p.Ala38Val; MODERATE	nonsynonymous_codon ; A38V	Average:11.968; most accessible tissue: Callus, score: 30.963	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408367682	3.34E-06	NA	mr1200	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