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Detailed information for vg0431157774:

Variant ID: vg0431157774 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31157774
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGATTAGATTAGAGATAGAGAAGAGATATATACTGATTAGAAATCGAAATTTGTTTAGCTCTTTCCATTTTTTTCTCGCGTGCATTTTTTATTTTGTA[C/A]
GAACCAGCTTTTTATTTTTTACGAACCATTTTTTTCGCCATTTTCTTAGGGAATCGGACGAACTTTTTTAAATGTTTTTTCAGATTTTTTCGTCTTTATA

Reverse complement sequence

TATAAAGACGAAAAAATCTGAAAAAACATTTAAAAAAGTTCGTCCGATTCCCTAAGAAAATGGCGAAAAAAATGGTTCGTAAAAAATAAAAAGCTGGTTC[G/T]
TACAAAATAAAAAATGCACGCGAGAAAAAAATGGAAAGAGCTAAACAAATTTCGATTTCTAATCAGTATATATCTCTTCTCTATCTCTAATCTAATCTAA

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	77.40%	0.30%	5.92%	16.42%	NA
All Indica	2759	68.50%	0.30%	5.87%	25.34%	NA
All Japonica	1512	89.10%	0.10%	7.21%	3.57%	NA
Aus	269	97.00%	0.70%	1.86%	0.37%	NA
Indica I	595	48.40%	0.30%	9.92%	41.34%	NA
Indica II	465	72.50%	0.20%	4.95%	22.37%	NA
Indica III	913	77.80%	0.20%	4.49%	17.52%	NA
Indica Intermediate	786	70.50%	0.50%	4.96%	24.05%	NA
Temperate Japonica	767	88.80%	0.30%	8.47%	2.48%	NA
Tropical Japonica	504	94.80%	0.00%	0.40%	4.76%	NA
Japonica Intermediate	241	78.00%	0.00%	17.43%	4.56%	NA
VI/Aromatic	96	83.30%	0.00%	3.12%	13.54%	NA
Intermediate	90	87.80%	1.10%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431157774	C -> DEL	N	N	silent_mutation	Average:12.229; most accessible tissue: Minghui63 flower, score: 19.775	N	N	N	N
vg0431157774	C -> A	LOC_Os04g52420.1	downstream_gene_variant ; 3088.0bp to feature; MODIFIER	silent_mutation	Average:12.229; most accessible tissue: Minghui63 flower, score: 19.775	N	N	N	N
vg0431157774	C -> A	LOC_Os04g52420-LOC_Os04g52440	intergenic_region ; MODIFIER	silent_mutation	Average:12.229; most accessible tissue: Minghui63 flower, score: 19.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431157774	7.33E-07	NA	mr1805_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
vg0431157774	5.28E-06	NA	mr1805_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