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Detailed information for vg1013084355:

Variant ID: vg1013084355 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13084355
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGACGGATGGATGAGGCTCAAACGCAGAATCGGACGGCCCGCAAGACGCCCAGCCAACAGCAACGTGTCGCAAGACGATTGGTCAACAGTAGCCAAATG[C/G]
CTGGGAGGCCGGCTAATCTAGCACCTTTAAGATATCTAGTATTCACATATGGTACTGCCTCCATCCAACTACAAATATATATAATCCTAAAGTTAAACTT

Reverse complement sequence

AAGTTTAACTTTAGGATTATATATATTTGTAGTTGGATGGAGGCAGTACCATATGTGAATACTAGATATCTTAAAGGTGCTAGATTAGCCGGCCTCCCAG[G/C]
CATTTGGCTACTGTTGACCAATCGTCTTGCGACACGTTGCTGTTGGCTGGGCGTCTTGCGGGCCGTCCGATTCTGCGTTTGAGCCTCATCCATCCGTCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.50%	20.90%	0.76%	11.85%	NA
All Indica	2759	61.10%	21.50%	1.05%	16.35%	NA
All Japonica	1512	91.40%	1.50%	0.26%	6.88%	NA
Aus	269	1.10%	98.50%	0.37%	0.00%	NA
Indica I	595	21.00%	20.20%	2.52%	56.30%	NA
Indica II	465	82.20%	8.80%	1.29%	7.74%	NA
Indica III	913	74.90%	24.20%	0.00%	0.88%	NA
Indica Intermediate	786	62.80%	27.00%	1.02%	9.16%	NA
Temperate Japonica	767	99.20%	0.40%	0.00%	0.39%	NA
Tropical Japonica	504	84.90%	2.40%	0.20%	12.50%	NA
Japonica Intermediate	241	80.10%	2.90%	1.24%	15.77%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	70.00%	22.20%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013084355	C -> G	LOC_Os10g25300.1	upstream_gene_variant ; 528.0bp to feature; MODIFIER	silent_mutation	Average:65.641; most accessible tissue: Minghui63 young leaf, score: 98.82	N	N	N	N
vg1013084355	C -> G	LOC_Os10g25310.1	upstream_gene_variant ; 4450.0bp to feature; MODIFIER	silent_mutation	Average:65.641; most accessible tissue: Minghui63 young leaf, score: 98.82	N	N	N	N
vg1013084355	C -> G	LOC_Os10g25300.2	upstream_gene_variant ; 528.0bp to feature; MODIFIER	silent_mutation	Average:65.641; most accessible tissue: Minghui63 young leaf, score: 98.82	N	N	N	N
vg1013084355	C -> G	LOC_Os10g25300-LOC_Os10g25310	intergenic_region ; MODIFIER	silent_mutation	Average:65.641; most accessible tissue: Minghui63 young leaf, score: 98.82	N	N	N	N
vg1013084355	C -> DEL	N	N	silent_mutation	Average:65.641; most accessible tissue: Minghui63 young leaf, score: 98.82	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)
vg1013084355	C	G	0.04	0.13	0.13	0.02	0.03	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013084355	NA	3.04E-09	mr1533	Ind_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
vg1013084355	NA	3.63E-09	mr1980	Ind_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
vg1013084355	1.58E-06	5.26E-13	mr1533_2	Ind_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
vg1013084355	NA	6.68E-06	mr1743_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
vg1013084355	9.21E-06	1.07E-09	mr1980_2	Ind_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