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Detailed information for vg0715976780:

Variant ID: vg0715976780 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15976780
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAATCCAACAGGTCGCGCAACCGATCCAGCAAACACCACCAAGTCGGCCGGTTGTACAGCCGATTCAGCAGACGCCGTTGAGACAGCAGGTCGTTCAG[T/C]
CGACTCGGCAGCAGGGCTTAATGGATGTATCAGCTGGATTCGCATCGCACGCTGGTCAGTGTGCTCCAAATCAGGTTGTCCCAGAGCACTTGATCCATCA

Reverse complement sequence

TGATGGATCAAGTGCTCTGGGACAACCTGATTTGGAGCACACTGACCAGCGTGCGATGCGAATCCAGCTGATACATCCATTAAGCCCTGCTGCCGAGTCG[A/G]
CTGAACGACCTGCTGTCTCAACGGCGTCTGCTGAATCGGCTGTACAACCGGCCGACTTGGTGGTGTTTGCTGGATCGGTTGCGCGACCTGTTGGATTGGG

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	36.00%	35.30%	5.88%	22.81%	NA
All Indica	2759	47.90%	4.20%	9.68%	38.17%	NA
All Japonica	1512	6.40%	92.90%	0.07%	0.66%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	53.60%	1.80%	12.94%	31.60%	NA
Indica II	465	17.40%	5.60%	6.67%	70.32%	NA
Indica III	913	57.10%	1.40%	9.20%	32.31%	NA
Indica Intermediate	786	51.00%	8.50%	9.54%	30.92%	NA
Temperate Japonica	767	11.20%	87.90%	0.00%	0.91%	NA
Tropical Japonica	504	1.60%	98.00%	0.20%	0.20%	NA
Japonica Intermediate	241	1.20%	97.90%	0.00%	0.83%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	23.30%	48.90%	11.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715976780	T -> DEL	LOC_Os07g27420.1	N	frameshift_variant	Average:22.723; most accessible tissue: Callus, score: 47.93	N	N	N	N
vg0715976780	T -> C	LOC_Os07g27420.1	missense_variant ; p.Ser438Pro; MODERATE	nonsynonymous_codon ; S438P	Average:22.723; most accessible tissue: Callus, score: 47.93	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715976780	3.93E-06	2.10E-07	mr1344	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
vg0715976780	NA	1.23E-10	mr1630	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
vg0715976780	NA	1.20E-06	mr1265_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
vg0715976780	5.83E-06	5.83E-06	mr1453_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
vg0715976780	5.25E-06	5.25E-06	mr1528_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