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Detailed information for vg0323605084:

Variant ID: vg0323605084 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23605084
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

ACATCAACCAGTACTAAAGATAGATTTTTACTCCCGGTTATTTCACCCGGGACTAAAGATAGCGATTTTTAGTCTCGGATTCGTAGTCCCGGTTGGAAAA[C/T]
CGGGACTAAAGTGGGGTTACGAATCGAGAGTAAAAACTACTTCTCCACCAGTGTGACAACTCAGCTAAGAGCGTGCCCCAGTTTGGTTTCTCGAGTCCAA

Reverse complement sequence

TTGGACTCGAGAAACCAAACTGGGGCACGCTCTTAGCTGAGTTGTCACACTGGTGGAGAAGTAGTTTTTACTCTCGATTCGTAACCCCACTTTAGTCCCG[G/A]
TTTTCCAACCGGGACTACGAATCCGAGACTAAAAATCGCTATCTTTAGTCCCGGGTGAAATAACCGGGAGTAAAAATCTATCTTTAGTACTGGTTGATGT

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	53.90%	45.80%	0.32%	0.00%	NA
All Indica	2759	80.40%	19.20%	0.43%	0.00%	NA
All Japonica	1512	0.80%	99.10%	0.13%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	67.90%	31.40%	0.67%	0.00%	NA
Indica II	465	80.90%	18.90%	0.22%	0.00%	NA
Indica III	913	89.00%	10.50%	0.44%	0.00%	NA
Indica Intermediate	786	79.50%	20.10%	0.38%	0.00%	NA
Temperate Japonica	767	0.30%	99.60%	0.13%	0.00%	NA
Tropical Japonica	504	1.20%	98.60%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	43.30%	55.60%	1.11%	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
vg0323605084	C -> T	LOC_Os03g42420.1	upstream_gene_variant ; 4687.0bp to feature; MODIFIER	silent_mutation	Average:58.953; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0323605084	C -> T	LOC_Os03g42410-LOC_Os03g42420	intergenic_region ; MODIFIER	silent_mutation	Average:58.953; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323605084	NA	5.97E-12	mr1553	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
vg0323605084	NA	1.06E-08	mr1322_2	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
vg0323605084	NA	4.02E-17	mr1553_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
vg0323605084	NA	1.13E-06	mr1553_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