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Detailed information for vg0208628363:

Variant ID: vg0208628363 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8628363
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.34, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

AAATATTGCGTACTTTTGTAGATACATGCCGGATGTATCTACGAAATTAGTAGATCAATTTGAAAAACCAATCTACCAATTACCTTATTGCGTACTCGTT[T/C]
GACATGATCTGACATCTTTTGGTACGCCGCGTATCTTGAGGCTTGGGTGAACTCGATAGACCAAGTTGTCGATGACGATGATGGTTCCGATCTCGTCGGA

Reverse complement sequence

TCCGACGAGATCGGAACCATCATCGTCATCGACAACTTGGTCTATCGAGTTCACCCAAGCCTCAAGATACGCGGCGTACCAAAAGATGTCAGATCATGTC[A/G]
AACGAGTACGCAATAAGGTAATTGGTAGATTGGTTTTTCAAATTGATCTACTAATTTCGTAGATACATCCGGCATGTATCTACAAAAGTACGCAATATTT

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	23.70%	21.10%	0.32%	54.91%	NA
All Indica	2759	8.50%	26.80%	0.47%	64.23%	NA
All Japonica	1512	56.30%	1.20%	0.13%	42.39%	NA
Aus	269	3.70%	69.90%	0.00%	26.39%	NA
Indica I	595	15.30%	16.50%	0.84%	67.39%	NA
Indica II	465	5.20%	37.20%	0.43%	57.20%	NA
Indica III	913	0.90%	31.20%	0.11%	67.80%	NA
Indica Intermediate	786	14.20%	23.30%	0.64%	61.83%	NA
Temperate Japonica	767	81.50%	0.40%	0.00%	18.12%	NA
Tropical Japonica	504	28.60%	2.00%	0.20%	69.25%	NA
Japonica Intermediate	241	34.00%	2.10%	0.41%	63.49%	NA
VI/Aromatic	96	1.00%	24.00%	0.00%	75.00%	NA
Intermediate	90	23.30%	33.30%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208628363	T -> DEL	LOC_Os02g15420.1	N	frameshift_variant	Average:12.229; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0208628363	T -> C	LOC_Os02g15420.1	synonymous_variant ; p.Ser61Ser; LOW	synonymous_codon	Average:12.229; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208628363	1.27E-06	1.27E-06	mr1159_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
vg0208628363	4.14E-06	4.14E-06	mr1286_2	Jap_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
vg0208628363	7.76E-06	7.75E-06	mr1373_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