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Detailed information for vg0404000463:

Variant ID: vg0404000463 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4000463
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGAGGTATCAAAACCATAAGGTTGGAGGGAAACACCACATCCCTAAGATGAATAGGTACGTCGATGCAAGCATGGCTTACGGTTACCTCACCCCCAGG[C/T]
GAGTGTACTATCATAGGCTTTCTAACTCCTACCAGAGTTAAGTTGTGCTGTTGACTAGCCTCCAGGGATATGAATGAATGCGATGCACCAGAATCGAGGA

Reverse complement sequence

TCCTCGATTCTGGTGCATCGCATTCATTCATATCCCTGGAGGCTAGTCAACAGCACAACTTAACTCTGGTAGGAGTTAGAAAGCCTATGATAGTACACTC[G/A]
CCTGGGGGTGAGGTAACCGTAAGCCATGCTTGCATCGACGTACCTATTCATCTTAGGGATGTGGTGTTTCCCTCCAACCTTATGGTTTTGATACCTCAGA

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	46.00%	43.50%	4.59%	5.95%	NA
All Indica	2759	26.40%	67.10%	5.91%	0.62%	NA
All Japonica	1512	76.30%	3.60%	2.71%	17.33%	NA
Aus	269	55.00%	42.40%	2.60%	0.00%	NA
Indica I	595	44.40%	52.40%	3.19%	0.00%	NA
Indica II	465	34.60%	55.10%	9.68%	0.65%	NA
Indica III	913	8.50%	84.80%	6.13%	0.55%	NA
Indica Intermediate	786	28.80%	64.60%	5.47%	1.15%	NA
Temperate Japonica	767	69.10%	0.90%	1.96%	28.03%	NA
Tropical Japonica	504	84.30%	6.50%	3.77%	5.36%	NA
Japonica Intermediate	241	82.60%	6.20%	2.90%	8.30%	NA
VI/Aromatic	96	95.80%	2.10%	0.00%	2.08%	NA
Intermediate	90	55.60%	37.80%	6.67%	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
vg0404000463	C -> DEL	LOC_Os04g07510.1	N	frameshift_variant	Average:12.918; most accessible tissue: Callus, score: 57.086	N	N	N	N
vg0404000463	C -> T	LOC_Os04g07510.1	synonymous_variant ; p.Ser348Ser; LOW	synonymous_codon	Average:12.918; most accessible tissue: Callus, score: 57.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404000463	7.00E-06	NA	mr1120	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
vg0404000463	NA	1.03E-07	mr1557	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
vg0404000463	NA	7.06E-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
vg0404000463	NA	1.95E-06	mr1540_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