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Detailed information for vg0401348208:

Variant ID: vg0401348208 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1348208
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.10, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGGACAACCTATTCCGGAGGTCATTTGGCGGAATTGTATATGGCAAGGATTGTGTGTTTGCATGGTGTTCCTAAGAAAATAGTATCCGATCGAGGTAG[T/C]
CAGTTTACTTCAAAGTTTTGGAAGAAGCTTCAGGAAGAGATGGGTTCTAAATTGAATTTCAGTACCGCATATCATCCACAGACAGACGGACAAACTGAAA

Reverse complement sequence

TTTCAGTTTGTCCGTCTGTCTGTGGATGATATGCGGTACTGAAATTCAATTTAGAACCCATCTCTTCCTGAAGCTTCTTCCAAAACTTTGAAGTAAACTG[A/G]
CTACCTCGATCGGATACTATTTTCTTAGGAACACCATGCAAACACACAATCCTTGCCATATACAATTCCGCCAAATGACCTCCGGAATAGGTTGTCCTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.40%	15.10%	37.45%	17.08%	NA
All Indica	2759	22.50%	20.70%	52.92%	3.95%	NA
All Japonica	1512	46.20%	1.50%	8.27%	43.98%	NA
Aus	269	22.30%	33.80%	43.12%	0.74%	NA
Indica I	595	15.00%	10.30%	72.10%	2.69%	NA
Indica II	465	23.20%	16.30%	54.19%	6.24%	NA
Indica III	913	25.60%	32.70%	38.01%	3.61%	NA
Indica Intermediate	786	24.00%	17.00%	54.96%	3.94%	NA
Temperate Japonica	767	54.50%	0.40%	4.17%	40.94%	NA
Tropical Japonica	504	36.70%	3.00%	13.69%	46.63%	NA
Japonica Intermediate	241	39.80%	2.10%	9.96%	48.13%	NA
VI/Aromatic	96	19.80%	16.70%	42.71%	20.83%	NA
Intermediate	90	42.20%	14.40%	31.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401348208	T -> C	LOC_Os04g03190.1	synonymous_variant ; p.Ser1026Ser; LOW	synonymous_codon	Average:8.315; most accessible tissue: Callus, score: 36.88	N	N	N	N
vg0401348208	T -> DEL	LOC_Os04g03190.1	N	frameshift_variant	Average:8.315; most accessible tissue: Callus, score: 36.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401348208	NA	1.31E-06	mr1805	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
vg0401348208	NA	1.90E-06	mr1880	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
vg0401348208	NA	3.21E-06	mr1544_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
vg0401348208	7.16E-07	NA	mr1879_2	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