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Detailed information for vg0301847279:

Variant ID: vg0301847279 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1847279
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTATATAAAAGGTACTTAAAAATTAAATAATATATTTGTCAAAATTTTAATAATTAATAGTCATTTAATTATATACTAACCACTTTTTTCGTTTGTGA[G/A]
CCGCTAATCAGCCCAAATTCATGTACCACAAAGAACACATTATAATTATTTTTTTCATTGGTAGGCAAGGTATCAATCAAGAGTAAATCAATTGTGGTGG

Reverse complement sequence

CCACCACAATTGATTTACTCTTGATTGATACCTTGCCTACCAATGAAAAAAATAATTATAATGTGTTCTTTGTGGTACATGAATTTGGGCTGATTAGCGG[C/T]
TCACAAACGAAAAAAGTGGTTAGTATATAATTAAATGACTATTAATTATTAAAATTTTGACAAATATATTATTTAATTTTTAAGTACCTTTTATATAGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.20%	0.50%	2.22%	3.07%	NA
All Indica	2759	98.70%	0.10%	0.54%	0.58%	NA
All Japonica	1512	99.50%	0.20%	0.20%	0.13%	NA
Aus	269	27.90%	5.90%	28.62%	37.55%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.10%	0.20%	0.43%	0.22%	NA
Indica III	913	98.90%	0.10%	0.44%	0.55%	NA
Indica Intermediate	786	97.50%	0.30%	1.15%	1.15%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	0.83%	0.83%	NA
VI/Aromatic	96	64.60%	2.10%	8.33%	25.00%	NA
Intermediate	90	95.60%	0.00%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301847279	G -> A	LOC_Os03g04040.1	downstream_gene_variant ; 1987.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301847279	G -> A	LOC_Os03g04040-LOC_Os03g04050	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301847279	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0301847279	G	A	0.0	0.0	0.0	0.0	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301847279	NA	1.31E-06	mr1126	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
vg0301847279	NA	3.18E-14	mr1231	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
vg0301847279	NA	7.31E-13	mr1409	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
vg0301847279	NA	4.20E-06	mr1523	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
vg0301847279	NA	2.36E-06	mr1652	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
vg0301847279	NA	4.57E-06	mr1528_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
vg0301847279	2.55E-06	NA	mr1889_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
vg0301847279	2.51E-06	NA	mr1896_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
vg0301847279	5.65E-06	NA	mr1907_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