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Detailed information for vg0330653946:

Variant ID: vg0330653946 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 30653946
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGATCATCCGCCCCTGACAACACGAGTCGGCCCAGCCGAAAGGTGCAGCGGCCCGTCTACTTTGTCAGCGAGGCGCTTCGGGATGCGAAGACCCGATAC[C/T]
TGCAGGCCTAGAAAATGCTTTATGCGGTTTTGATGGCCTCAAGGAAATTGCGCCACTATTTCCAAGCGCATCGGGTTTCCGTGGTGACATCCTACCCTCT

Reverse complement sequence

AGAGGGTAGGATGTCACCACGGAAACCCGATGCGCTTGGAAATAGTGGCGCAATTTCCTTGAGGCCATCAAAACCGCATAAAGCATTTTCTAGGCCTGCA[G/A]
GTATCGGGTCTTCGCATCCCGAAGCGCCTCGCTGACAAAGTAGACGGGCCGCTGCACCTTTCGGCTGGGCCGACTCGTGTTGTCAGGGGCGGATGATCTG

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	95.70%	3.70%	0.53%	0.00%	NA
All Indica	2759	92.80%	6.30%	0.87%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.60%	4.70%	1.68%	0.00%	NA
Indica II	465	90.10%	9.00%	0.86%	0.00%	NA
Indica III	913	96.60%	3.30%	0.11%	0.00%	NA
Indica Intermediate	786	89.40%	9.40%	1.15%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0330653946	C -> T	LOC_Os03g53430.1	intron_variant ; MODIFIER	silent_mutation	Average:60.28; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0330653946	NA	8.34E-06	mr1261	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
vg0330653946	9.40E-08	9.39E-08	mr1360	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