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Detailed information for vg0324122964:

Variant ID: vg0324122964 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24122964
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATCAGCCTGATCGATCCCAAATTCGACTGGCAAGGTAAAAACCATGTTAATTGATGCTGTTACCACACTTTTCCCTTTTGCCAACATCTCTGCCTCAT[C/T]
GGCTACGACATCATCGGCCCCAAAAGCTTGACCCTTAACACGCCACTCCTGCTTCGGTTTTGCCTTCCTTAGCCGATGATTAATTTCTTGCTCGACCTCC

Reverse complement sequence

GGAGGTCGAGCAAGAAATTAATCATCGGCTAAGGAAGGCAAAACCGAAGCAGGAGTGGCGTGTTAAGGGTCAAGCTTTTGGGGCCGATGATGTCGTAGCC[G/A]
ATGAGGCAGAGATGTTGGCAAAAGGGAAAAGTGTGGTAACAGCATCAATTAACATGGTTTTTACCTTGCCAGTCGAATTTGGGATCGATCAGGCTGATGT

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	75.50%	10.30%	5.92%	8.25%	NA
All Indica	2759	63.60%	16.20%	7.25%	12.90%	NA
All Japonica	1512	99.60%	0.00%	0.07%	0.33%	NA
Aus	269	54.60%	13.00%	26.39%	5.95%	NA
Indica I	595	42.90%	17.10%	8.57%	31.43%	NA
Indica II	465	86.00%	2.40%	4.30%	7.31%	NA
Indica III	913	64.20%	23.10%	7.78%	4.93%	NA
Indica Intermediate	786	65.40%	15.80%	7.38%	11.45%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	92.70%	2.10%	2.08%	3.12%	NA
Intermediate	90	80.00%	2.20%	6.67%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324122964	C -> T	LOC_Os03g43270.1	missense_variant ; p.Asp867Asn; MODERATE	nonsynonymous_codon ; D867N	Average:16.758; most accessible tissue: Callus, score: 43.151	possibly damaging	1.819	TOLERATED	0.07
vg0324122964	C -> DEL	LOC_Os03g43270.1	N	frameshift_variant	Average:16.758; most accessible tissue: Callus, score: 43.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324122964	2.96E-06	NA	mr1874	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
vg0324122964	NA	3.12E-07	mr1874	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