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Detailed information for vg0430646747:

Variant ID: vg0430646747 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30646747
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, C: 0.17, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ACCCGATGAGGGTTACGACAGATTGGTTTAGGTTTTCTCGATTAAGATGTAAATTTTTTAAACTGTGAAATATTATGTTTTTAAAATAAAACTTTTTTAA[C/A]
TATCAAATAAATCTATCTTTTAAATTTATAATAATTATAACTCAATTAATTACACACGGTTGGTTTTCTCGTTTTGCATGCTCTGACTTCATTTTTAATC

Reverse complement sequence

GATTAAAAATGAAGTCAGAGCATGCAAAACGAGAAAACCAACCGTGTGTAATTAATTGAGTTATAATTATTATAAATTTAAAAGATAGATTTATTTGATA[G/T]
TTAAAAAAGTTTTATTTTAAAAACATAATATTTCACAGTTTAAAAAATTTACATCTTAATCGAGAAAACCTAAACCAATCTGTCGTAACCCTCATCGGGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.90%	25.10%	0.08%	0.00%	NA
All Indica	2759	97.30%	2.70%	0.00%	0.00%	NA
All Japonica	1512	41.60%	58.20%	0.20%	0.00%	NA
Aus	269	23.80%	76.20%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.50%	0.00%	0.00%	NA
Temperate Japonica	767	31.40%	68.40%	0.13%	0.00%	NA
Tropical Japonica	504	61.70%	38.10%	0.20%	0.00%	NA
Japonica Intermediate	241	32.00%	67.60%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	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
vg0430646747	C -> A	LOC_Os04g51710.1	upstream_gene_variant ; 902.0bp to feature; MODIFIER	silent_mutation	Average:53.052; most accessible tissue: Callus, score: 83.984	N	N	N	N
vg0430646747	C -> A	LOC_Os04g51720.1	upstream_gene_variant ; 2440.0bp to feature; MODIFIER	silent_mutation	Average:53.052; most accessible tissue: Callus, score: 83.984	N	N	N	N
vg0430646747	C -> A	LOC_Os04g51710-LOC_Os04g51720	intergenic_region ; MODIFIER	silent_mutation	Average:53.052; most accessible tissue: Callus, score: 83.984	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430646747	1.33E-15	1.16E-47	mr1745	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
vg0430646747	4.57E-06	5.56E-08	mr1745	Jap_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
vg0430646747	3.26E-06	NA	mr1042_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
vg0430646747	1.84E-09	NA	mr1064_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
vg0430646747	3.09E-07	1.08E-18	mr1167_2	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
vg0430646747	NA	1.66E-07	mr1167_2	Jap_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
vg0430646747	NA	2.80E-10	mr1228_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
vg0430646747	NA	1.91E-07	mr1269_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
vg0430646747	NA	4.74E-07	mr1479_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
vg0430646747	NA	1.40E-10	mr1667_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
vg0430646747	NA	3.27E-08	mr1677_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
vg0430646747	NA	3.58E-07	mr1704_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
vg0430646747	5.34E-06	NA	mr1726_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
vg0430646747	3.97E-24	1.22E-59	mr1745_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
vg0430646747	6.23E-09	5.58E-12	mr1745_2	Jap_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
vg0430646747	1.56E-06	NA	mr1871_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
vg0430646747	NA	1.61E-06	mr1910_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
vg0430646747	NA	3.73E-10	mr1940_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
vg0430646747	NA	4.41E-14	mr1950_2	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