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Detailed information for vg0729333582:

Variant ID: vg0729333582 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29333582
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.30, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTCACATGTAGATGAATTTGAATATTAGACTTTACACATCCTCTCTCCGTCACATAAAAAATAAATCTAGTACGAGATGTGACACAAATTAGTACTA[T/C]
AAATTTGACCACTGAAAAATTATTCGTGTGTTTCAAAATATATTGGGGCTAAAGAAAATAAAGTTAAGCATAGCGGACCTGTTGGAGGGACCTGCTCACA

Reverse complement sequence

TGTGAGCAGGTCCCTCCAACAGGTCCGCTATGCTTAACTTTATTTTCTTTAGCCCCAATATATTTTGAAACACACGAATAATTTTTCAGTGGTCAAATTT[A/G]
TAGTACTAATTTGTGTCACATCTCGTACTAGATTTATTTTTTATGTGACGGAGAGAGGATGTGTAAAGTCTAATATTCAAATTCATCTACATGTGAAGAA

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	63.90%	36.10%	0.00%	0.00%	NA
All Indica	2759	95.30%	4.70%	0.00%	0.00%	NA
All Japonica	1512	11.60%	88.40%	0.00%	0.00%	NA
Aus	269	62.50%	37.50%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	93.30%	6.70%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.50%	0.00%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	19.60%	80.40%	0.00%	0.00%	NA
Japonica Intermediate	241	29.00%	71.00%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	43.30%	56.70%	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
vg0729333582	T -> C	LOC_Os07g49000.1	upstream_gene_variant ; 4865.0bp to feature; MODIFIER	silent_mutation	Average:57.422; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0729333582	T -> C	LOC_Os07g48980-LOC_Os07g49000	intergenic_region ; MODIFIER	silent_mutation	Average:57.422; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729333582	NA	2.81E-07	mr1039	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
vg0729333582	NA	5.11E-06	mr1734	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