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Detailed information for vg0629600778:

Variant ID: vg0629600778 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29600778
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCCTTCTTCCTCCCTCTCTCCCCCTCTCTCCTCGGGAGGGACGCGCCGTCGCAGCCGTGGGCGGTGAAGGCAGCTGCAGACTCAACGCTGGCACTCAC[G/A]
GTGAGGGGGCAGTTGAGGCGGAGCCGCACCATCCTGCTGCGGCACCAGTGGGATGACGACAGGGAGCGGCGCTGATGAGGCTGCCGACGGCAAGCTTCGT

Reverse complement sequence

ACGAAGCTTGCCGTCGGCAGCCTCATCAGCGCCGCTCCCTGTCGTCATCCCACTGGTGCCGCAGCAGGATGGTGCGGCTCCGCCTCAACTGCCCCCTCAC[C/T]
GTGAGTGCCAGCGTTGAGTCTGCAGCTGCCTTCACCGCCCACGGCTGCGACGGCGCGTCCCTCCCGAGGAGAGAGGGGGAGAGAGGGAGGAAGAAGGGGT

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	83.00%	16.30%	0.74%	0.00%	NA
All Indica	2759	93.50%	6.40%	0.14%	0.00%	NA
All Japonica	1512	67.10%	31.30%	1.59%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	90.40%	9.20%	0.34%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	10.30%	0.25%	0.00%	NA
Temperate Japonica	767	94.90%	3.30%	1.83%	0.00%	NA
Tropical Japonica	504	26.40%	71.80%	1.79%	0.00%	NA
Japonica Intermediate	241	63.50%	36.10%	0.41%	0.00%	NA
VI/Aromatic	96	15.60%	83.30%	1.04%	0.00%	NA
Intermediate	90	72.20%	21.10%	6.67%	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
vg0629600778	G -> A	LOC_Os06g48880.1	upstream_gene_variant ; 2483.0bp to feature; MODIFIER	silent_mutation	Average:77.783; most accessible tissue: Minghui63 young leaf, score: 86.723	N	N	N	N
vg0629600778	G -> A	LOC_Os06g48900.1	upstream_gene_variant ; 4119.0bp to feature; MODIFIER	silent_mutation	Average:77.783; most accessible tissue: Minghui63 young leaf, score: 86.723	N	N	N	N
vg0629600778	G -> A	LOC_Os06g48880-LOC_Os06g48900	intergenic_region ; MODIFIER	silent_mutation	Average:77.783; most accessible tissue: Minghui63 young leaf, score: 86.723	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)
vg0629600778	G	A	0.0	-0.01	-0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629600778	9.14E-06	9.14E-06	mr1173	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
vg0629600778	5.56E-06	1.81E-08	mr1177	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
vg0629600778	NA	6.52E-08	mr1335_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
vg0629600778	NA	3.11E-07	mr1350_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
vg0629600778	NA	1.74E-09	mr1578_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
vg0629600778	NA	9.35E-06	mr1923_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
vg0629600778	NA	1.34E-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