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Detailed information for vg0624687317:

Variant ID: vg0624687317 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24687317
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGTTTTAGATCAAATTAAAGGTAAAACAGGATGTGTGATCTGCTCGAATGGAACGTACTATAGGTATCTCCCGGGTTCCAACAAGCTTGTGTACATG[C/T]
GGCACCGGCGGTTCCTACGCACAAATCACAAGTACCACAAGATGAAGGCAGAGTTCGATGGAACTGAAGAGACTGATCCTACACCAAAACCTACATCGGG

Reverse complement sequence

CCCGATGTAGGTTTTGGTGTAGGATCAGTCTCTTCAGTTCCATCGAACTCTGCCTTCATCTTGTGGTACTTGTGATTTGTGCGTAGGAACCGCCGGTGCC[G/A]
CATGTACACAAGCTTGTTGGAACCCGGGAGATACCTATAGTACGTTCCATTCGAGCAGATCACACATCCTGTTTTACCTTTAATTTGATCTAAAACTGAA

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	55.30%	44.60%	0.08%	0.00%	NA
All Indica	2759	91.10%	8.80%	0.11%	0.00%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	16.70%	83.30%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	93.10%	6.90%	0.00%	0.00%	NA
Indica III	913	87.60%	12.30%	0.11%	0.00%	NA
Indica Intermediate	786	87.50%	12.30%	0.13%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	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
vg0624687317	C -> T	LOC_Os06g41250.1	intron_variant ; MODIFIER	silent_mutation	Average:28.29; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624687317	NA	6.74E-08	mr1610	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
vg0624687317	9.45E-08	2.08E-06	mr1719	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
vg0624687317	NA	8.51E-07	mr1548_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