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Detailed information for vg0324209979:

Variant ID: vg0324209979 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24209979
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTAACCAACATATTTTAATATTGACAAAGTCACCGCAGTCATCTCGCTATCAACAGGCACGTCGATCACCTGCCACTAAAACAATTAATAGCTACAGA[C/T]
ATGAGCGTACTCATGTCAAATTTAGAACTTGAACTCTTATCTAGACGAGCAGGTTTCATCACAAGAAATCTAAGCAGCTGAGCTACGCTAAATTCGTGAA

Reverse complement sequence

TTCACGAATTTAGCGTAGCTCAGCTGCTTAGATTTCTTGTGATGAAACCTGCTCGTCTAGATAAGAGTTCAAGTTCTAAATTTGACATGAGTACGCTCAT[G/A]
TCTGTAGCTATTAATTGTTTTAGTGGCAGGTGATCGACGTGCCTGTTGATAGCGAGATGACTGCGGTGACTTTGTCAATATTAAAATATGTTGGTTAAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.20%	24.80%	1.69%	0.36%	NA
All Indica	2759	98.40%	1.20%	0.04%	0.33%	NA
All Japonica	1512	32.50%	62.30%	4.89%	0.33%	NA
Aus	269	62.10%	37.90%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.10%	0.40%	0.00%	0.44%	NA
Indica Intermediate	786	96.30%	3.10%	0.13%	0.51%	NA
Temperate Japonica	767	57.20%	36.00%	6.65%	0.13%	NA
Tropical Japonica	504	4.60%	92.50%	2.58%	0.40%	NA
Japonica Intermediate	241	12.00%	83.00%	4.15%	0.83%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	24.40%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324209979	C -> T	LOC_Os03g43410.1	upstream_gene_variant ; 2575.0bp to feature; MODIFIER	silent_mutation	Average:54.679; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0324209979	C -> T	LOC_Os03g43400-LOC_Os03g43410	intergenic_region ; MODIFIER	silent_mutation	Average:54.679; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0324209979	C -> DEL	N	N	silent_mutation	Average:54.679; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324209979	NA	2.05E-10	mr1486	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
vg0324209979	NA	4.48E-07	mr1548	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
vg0324209979	NA	1.48E-07	mr1010_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
vg0324209979	NA	2.88E-08	mr1084_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
vg0324209979	NA	1.81E-07	mr1205_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
vg0324209979	NA	8.26E-07	mr1263_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
vg0324209979	NA	7.68E-06	mr1379_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
vg0324209979	NA	4.30E-16	mr1454_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
vg0324209979	NA	3.36E-15	mr1486_2	Jap_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
vg0324209979	NA	3.52E-09	mr1588_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