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Detailed information for vg0311462737:

Variant ID: vg0311462737 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11462737
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGACTTCGTGGAAAGCTTATCTCGCTACCTTTCAAGCGCATCTGGTCTCATATCCAAATTCATCTCGAGTCAACGGGAATCGCCAAAACAAGACAGTG[T/C]
TGTTGATGAAACCAAACTTGGGCCTTGGGCCTTATAATAGACTAGTCCCTTCTCGGAAGTGTCTCCCTCCACCTCCACAAATTAGCACTTAACCCTAGCT

Reverse complement sequence

AGCTAGGGTTAAGTGCTAATTTGTGGAGGTGGAGGGAGACACTTCCGAGAAGGGACTAGTCTATTATAAGGCCCAAGGCCCAAGTTTGGTTTCATCAACA[A/G]
CACTGTCTTGTTTTGGCGATTCCCGTTGACTCGAGATGAATTTGGATATGAGACCAGATGCGCTTGAAAGGTAGCGAGATAAGCTTTCCACGAAGTCCAA

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	50.20%	49.60%	0.23%	0.00%	NA
All Indica	2759	27.20%	72.50%	0.29%	0.00%	NA
All Japonica	1512	98.60%	1.20%	0.20%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	69.20%	30.10%	0.67%	0.00%	NA
Indica II	465	8.40%	91.40%	0.22%	0.00%	NA
Indica III	913	7.80%	92.10%	0.11%	0.00%	NA
Indica Intermediate	786	29.10%	70.60%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.20%	0.40%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	0.00%	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
vg0311462737	T -> C	LOC_Os03g20290.1	upstream_gene_variant ; 4899.0bp to feature; MODIFIER	silent_mutation	Average:35.49; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0311462737	T -> C	LOC_Os03g20270.1	downstream_gene_variant ; 1690.0bp to feature; MODIFIER	silent_mutation	Average:35.49; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0311462737	T -> C	LOC_Os03g20280.1	intron_variant ; MODIFIER	silent_mutation	Average:35.49; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311462737	NA	6.07E-18	mr1557	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
vg0311462737	NA	5.04E-11	mr1232_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
vg0311462737	NA	2.04E-09	mr1347_2	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
vg0311462737	NA	3.23E-13	mr1553_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
vg0311462737	NA	2.34E-20	mr1557_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
vg0311462737	NA	1.60E-07	mr1557_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