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Detailed information for vg0404315243:

Variant ID: vg0404315243 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4315243
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAATTTAAAACTTGTTCTTGCAATTGGTATCAGCGAGGAAATAGATGTTGGGCACAAAGGAAAGCCAGATATTGCAGAGATGTCTGAGAAAAAATTCG[G/C]
CCAAACAAACTGTGATTTTGTTCCAGGCATTATCTTGAGCAACTGTTAAGCATGTAGTACCAATCAGATTATGCGCAGGCAACATCATAGACGAAGTTAT

Reverse complement sequence

ATAACTTCGTCTATGATGTTGCCTGCGCATAATCTGATTGGTACTACATGCTTAACAGTTGCTCAAGATAATGCCTGGAACAAAATCACAGTTTGTTTGG[C/G]
CGAATTTTTTCTCAGACATCTCTGCAATATCTGGCTTTCCTTTGTGCCCAACATCTATTTCCTCGCTGATACCAATTGCAAGAACAAGTTTTAAATTTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.10%	3.10%	2.18%	34.60%	NA
All Indica	2759	66.90%	3.10%	1.96%	28.02%	NA
All Japonica	1512	50.40%	0.20%	2.45%	46.96%	NA
Aus	269	43.50%	21.60%	1.86%	33.09%	NA
Indica I	595	90.60%	1.00%	0.34%	8.07%	NA
Indica II	465	81.90%	0.60%	1.72%	15.70%	NA
Indica III	913	41.30%	6.20%	3.07%	49.40%	NA
Indica Intermediate	786	70.00%	2.40%	2.04%	25.57%	NA
Temperate Japonica	767	65.70%	0.00%	1.69%	32.59%	NA
Tropical Japonica	504	21.80%	0.40%	4.37%	73.41%	NA
Japonica Intermediate	241	61.40%	0.40%	0.83%	37.34%	NA
VI/Aromatic	96	55.20%	0.00%	1.04%	43.75%	NA
Intermediate	90	67.80%	2.20%	6.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404315243	G -> C	LOC_Os04g08070.1	upstream_gene_variant ; 4795.0bp to feature; MODIFIER	silent_mutation	Average:41.107; most accessible tissue: Callus, score: 65.116	N	N	N	N
vg0404315243	G -> C	LOC_Os04g08080.1	downstream_gene_variant ; 3676.0bp to feature; MODIFIER	silent_mutation	Average:41.107; most accessible tissue: Callus, score: 65.116	N	N	N	N
vg0404315243	G -> C	LOC_Os04g08070-LOC_Os04g08080	intergenic_region ; MODIFIER	silent_mutation	Average:41.107; most accessible tissue: Callus, score: 65.116	N	N	N	N
vg0404315243	G -> DEL	N	N	silent_mutation	Average:41.107; most accessible tissue: Callus, score: 65.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404315243	NA	3.67E-06	mr1043_2	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
vg0404315243	6.50E-06	2.11E-06	mr1479_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