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Detailed information for vg0313459666:

Variant ID: vg0313459666 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13459666
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTAAATGAAGAAATTCGTAAATATCCATTTAAAGAGCATATAAACTTCAAATGGCCATACCTTGGCCATTTGAACTCGGAATTGGACCGTTCAAGTC[C/T]
CTAATTTTTCCTTAAGATGTAAAGAACCCATTTTTGTGCTTTGTTTCTGCTGTTATGTGGAGTTATTTAGTGGTTAAGCCTTTTCTTTTCCGTTGGTCGT

Reverse complement sequence

ACGACCAACGGAAAAGAAAAGGCTTAACCACTAAATAACTCCACATAACAGCAGAAACAAAGCACAAAAATGGGTTCTTTACATCTTAAGGAAAAATTAG[G/A]
GACTTGAACGGTCCAATTCCGAGTTCAAATGGCCAAGGTATGGCCATTTGAAGTTTATATGCTCTTTAAATGGATATTTACGAATTTCTTCATTTAAATT

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	23.80%	21.30%	25.62%	29.22%	NA
All Indica	2759	8.30%	35.30%	33.89%	22.51%	NA
All Japonica	1512	56.80%	0.70%	5.69%	36.84%	NA
Aus	269	3.70%	1.90%	50.19%	44.24%	NA
Indica I	595	18.80%	14.80%	40.67%	25.71%	NA
Indica II	465	6.50%	9.20%	38.92%	45.38%	NA
Indica III	913	1.50%	65.80%	25.85%	6.79%	NA
Indica Intermediate	786	9.20%	30.90%	35.11%	24.81%	NA
Temperate Japonica	767	93.70%	0.10%	0.39%	5.74%	NA
Tropical Japonica	504	13.50%	1.60%	12.90%	72.02%	NA
Japonica Intermediate	241	29.90%	0.40%	7.47%	62.24%	NA
VI/Aromatic	96	2.10%	7.30%	29.17%	61.46%	NA
Intermediate	90	28.90%	13.30%	30.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0313459666	C -> T	LOC_Os03g23760.1	upstream_gene_variant ; 727.0bp to feature; MODIFIER	silent_mutation	Average:31.098; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0313459666	C -> T	LOC_Os03g23250.1	downstream_gene_variant ; 1529.0bp to feature; MODIFIER	silent_mutation	Average:31.098; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0313459666	C -> T	LOC_Os03g23250-LOC_Os03g23760	intergenic_region ; MODIFIER	silent_mutation	Average:31.098; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0313459666	C -> DEL	N	N	silent_mutation	Average:31.098; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313459666	NA	6.92E-07	mr1668	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
vg0313459666	NA	1.51E-10	mr1712	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
vg0313459666	NA	9.90E-13	mr1844	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
vg0313459666	NA	5.01E-06	mr1871	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
vg0313459666	NA	1.41E-07	mr1977	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
vg0313459666	NA	8.40E-21	mr1361_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
vg0313459666	NA	6.79E-06	mr1695_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
vg0313459666	NA	2.00E-06	mr1730_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
vg0313459666	1.46E-07	NA	mr1842_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
vg0313459666	NA	1.04E-06	mr1860_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
vg0313459666	NA	4.91E-06	mr1866_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
vg0313459666	NA	3.85E-09	mr1952_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