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Detailed information for vg0401709977:

Variant ID: vg0401709977 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1709977
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: 51. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCAAATTTCAAGGGGGCTACCTATTTGGGAGCCTAGCATGGTATGATGGAGGCACTCACTATGTCAGGATTCCAATTGCGGTTCGACCAATAGTATCC[G/A]
ATAATTATGCAGATCTCTGAAGAAGCATAGAACTACAGAATGTTCATACTTCAAAAGGTTCTGTGGAGCAGGCCTCATCCTATATTATCCCCTCAAAGTT

Reverse complement sequence

AACTTTGAGGGGATAATATAGGATGAGGCCTGCTCCACAGAACCTTTTGAAGTATGAACATTCTGTAGTTCTATGCTTCTTCAGAGATCTGCATAATTAT[C/T]
GGATACTATTGGTCGAACCGCAATTGGAATCCTGACATAGTGAGTGCCTCCATCATACCATGCTAGGCTCCCAAATAGGTAGCCCCCTTGAAATTTGCGG

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	38.30%	1.10%	10.66%	49.89%	NA
All Indica	2759	26.40%	1.50%	9.60%	62.52%	NA
All Japonica	1512	60.00%	0.40%	6.94%	32.67%	NA
Aus	269	33.50%	1.50%	33.09%	31.97%	NA
Indica I	595	11.80%	2.20%	9.75%	76.30%	NA
Indica II	465	42.60%	1.70%	6.88%	48.82%	NA
Indica III	913	24.80%	0.40%	13.47%	61.34%	NA
Indica Intermediate	786	29.80%	2.00%	6.62%	61.58%	NA
Temperate Japonica	767	80.70%	0.10%	3.26%	15.91%	NA
Tropical Japonica	504	31.90%	1.00%	14.09%	52.98%	NA
Japonica Intermediate	241	52.70%	0.00%	3.73%	43.57%	NA
VI/Aromatic	96	51.00%	1.00%	35.42%	12.50%	NA
Intermediate	90	41.10%	1.10%	12.22%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401709977	G -> DEL	LOC_Os04g03796.2	N	frameshift_variant	Average:57.21; most accessible tissue: Callus, score: 87.506	N	N	N	N
vg0401709977	G -> DEL	LOC_Os04g03796.1	N	frameshift_variant	Average:57.21; most accessible tissue: Callus, score: 87.506	N	N	N	N
vg0401709977	G -> A	LOC_Os04g03796.1	missense_variant ; p.Asp770Asn; MODERATE	nonsynonymous_codon ; D770N	Average:57.21; most accessible tissue: Callus, score: 87.506	unknown	unknown	TOLERATED	0.09
vg0401709977	G -> A	LOC_Os04g03796.2	missense_variant ; p.Asp410Asn; MODERATE	nonsynonymous_codon ; D410N	Average:57.21; most accessible tissue: Callus, score: 87.506	unknown	unknown	TOLERATED	0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401709977	NA	8.71E-06	mr1411	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
vg0401709977	NA	1.83E-08	mr1565	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
vg0401709977	NA	2.71E-07	mr1715	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
vg0401709977	NA	2.31E-07	mr1748	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
vg0401709977	NA	1.46E-06	mr1062_2	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