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Detailed information for vg0324748140:

Variant ID: vg0324748140 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24748140
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAAGTACTGTAGATAATAAAGTAAGTCACAAATAAAATAAATAATAATTTCAAAAAAATTTGAATAAGACGAGTGGTCAAACATTACAAGCAAAAACT[T/C]
AAAATCCCTTATGTTATGGGACGGAGGGAGTACATGTTAGTTCAGTGTGTTGACTTGGTCTGAATACATATTTGAATCGCCCTGTAAATAGTAGAAAAGG

Reverse complement sequence

CCTTTTCTACTATTTACAGGGCGATTCAAATATGTATTCAGACCAAGTCAACACACTGAACTAACATGTACTCCCTCCGTCCCATAACATAAGGGATTTT[A/G]
AGTTTTTGCTTGTAATGTTTGACCACTCGTCTTATTCAAATTTTTTTGAAATTATTATTTATTTTATTTGTGACTTACTTTATTATCTACAGTACTTTAA

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	83.80%	15.80%	0.32%	0.00%	NA
All Indica	2759	81.40%	18.10%	0.47%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	17.10%	82.50%	0.37%	0.00%	NA
Indica I	595	84.20%	14.50%	1.34%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	67.70%	32.20%	0.11%	0.00%	NA
Indica Intermediate	786	86.10%	13.40%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	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
vg0324748140	T -> C	LOC_Os03g44030.1	upstream_gene_variant ; 4709.0bp to feature; MODIFIER	silent_mutation	Average:41.872; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0324748140	T -> C	LOC_Os03g44020.1	downstream_gene_variant ; 2406.0bp to feature; MODIFIER	silent_mutation	Average:41.872; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0324748140	T -> C	LOC_Os03g44020-LOC_Os03g44030	intergenic_region ; MODIFIER	silent_mutation	Average:41.872; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324748140	NA	4.95E-09	mr1388_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
vg0324748140	NA	8.14E-08	mr1522_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
vg0324748140	4.32E-06	1.46E-06	mr1817_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