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Detailed information for vg0414331250:

Variant ID: vg0414331250 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14331250
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGCGGACTGTAAGAAGTACTTGTGAAATAGAAAGGAAATCTATCTAACTAAGCTTTCTTACTCTGGATGCTGTGTGTACGAGTGTCTTCTCACTTTG[T/C]
GACTTCGATTAGTCACTTGAGTCATACACTCTCCCTAACCCCCAGCCTTGTCATCGGAGAATTCTTCTTGGAAGATATGGCTTTTGGACCTTTGACCTGC

Reverse complement sequence

GCAGGTCAAAGGTCCAAAAGCCATATCTTCCAAGAAGAATTCTCCGATGACAAGGCTGGGGGTTAGGGAGAGTGTATGACTCAAGTGACTAATCGAAGTC[A/G]
CAAAGTGAGAAGACACTCGTACACACAGCATCCAGAGTAAGAAAGCTTAGTTAGATAGATTTCCTTTCTATTTCACAAGTACTTCTTACAGTCCGCAAAA

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	59.30%	19.60%	10.39%	10.73%	NA
All Indica	2759	47.80%	22.30%	16.71%	13.16%	NA
All Japonica	1512	90.00%	0.50%	0.79%	8.66%	NA
Aus	269	4.80%	95.20%	0.00%	0.00%	NA
Indica I	595	56.00%	11.10%	21.01%	11.93%	NA
Indica II	465	22.20%	35.30%	23.01%	19.57%	NA
Indica III	913	59.40%	23.80%	8.54%	8.32%	NA
Indica Intermediate	786	43.40%	21.50%	19.21%	15.90%	NA
Temperate Japonica	767	91.70%	0.10%	0.26%	7.95%	NA
Tropical Japonica	504	90.30%	1.00%	1.59%	7.14%	NA
Japonica Intermediate	241	84.20%	0.80%	0.83%	14.11%	NA
VI/Aromatic	96	53.10%	33.30%	8.33%	5.21%	NA
Intermediate	90	66.70%	13.30%	11.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414331250	T -> C	LOC_Os04g24860.1	downstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:14.981; most accessible tissue: Callus, score: 32.062	N	N	N	N
vg0414331250	T -> C	LOC_Os04g24870.1	downstream_gene_variant ; 459.0bp to feature; MODIFIER	silent_mutation	Average:14.981; most accessible tissue: Callus, score: 32.062	N	N	N	N
vg0414331250	T -> C	LOC_Os04g24880.1	downstream_gene_variant ; 2029.0bp to feature; MODIFIER	silent_mutation	Average:14.981; most accessible tissue: Callus, score: 32.062	N	N	N	N
vg0414331250	T -> C	LOC_Os04g24860-LOC_Os04g24870	intergenic_region ; MODIFIER	silent_mutation	Average:14.981; most accessible tissue: Callus, score: 32.062	N	N	N	N
vg0414331250	T -> DEL	N	N	silent_mutation	Average:14.981; most accessible tissue: Callus, score: 32.062	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414331250	NA	4.78E-06	mr1130	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
vg0414331250	NA	1.14E-07	mr1877	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