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Detailed information for vg0404247363:

Variant ID: vg0404247363 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4247363
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGATTGCCTGATGGGCTGACCGTTGGAGGAGGTATGTACGGCTGGGGATCCTGGGACCGATGTGCTGC[C/A,T]
ATCCGTTAATCCACCTTCCTTGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCTGTACTCAAGATCTGCAATCTTCGTCCCGGTATCTCTCT

Reverse complement sequence

AGAGAGATACCGGGACGAAGATTGCAGATCTTGAGTACAGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCAAGGAAGGTGGATTAACGGAT[G/T,A]
GCAGCACATCGGTCCCAGGATCCCCAGCCGTACATACCTCCTCCAACGGTCAGCCCATCAGGCAATCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.90%	36.50%	1.40%	4.23%	NA
All Indica	2759	31.30%	59.50%	2.17%	7.07%	NA
All Japonica	1512	99.10%	0.80%	0.13%	0.00%	NA
Aus	269	84.40%	13.00%	1.49%	1.12%	NA
Indica I	595	9.60%	74.60%	4.37%	11.43%	NA
Indica II	465	35.30%	59.40%	1.51%	3.87%	NA
Indica III	913	37.00%	55.00%	1.53%	6.46%	NA
Indica Intermediate	786	38.70%	53.30%	1.65%	6.36%	NA
Temperate Japonica	767	99.30%	0.40%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	35.60%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404247363	C -> DEL	N	N	silent_mutation	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> A	LOC_Os04g07970.1	upstream_gene_variant ; 3401.0bp to feature; MODIFIER	silent_mutation	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> A	LOC_Os04g07990.1	downstream_gene_variant ; 3413.0bp to feature; MODIFIER	silent_mutation	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> A	LOC_Os04g07980.1	intron_variant ; MODIFIER	silent_mutation	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> T	LOC_Os04g07970.1	upstream_gene_variant ; 3401.0bp to feature; MODIFIER	N	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> T	LOC_Os04g07990.1	downstream_gene_variant ; 3413.0bp to feature; MODIFIER	N	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N
vg0404247363	C -> T	LOC_Os04g07980.1	intron_variant ; MODIFIER	N	Average:56.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.526	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404247363	1.25E-06	3.34E-06	mr1952	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