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Detailed information for vg0103512299:

Variant ID: vg0103512299 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3512299
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGAGGCTGTCGCCGCCGGCGCTCGTGCCCAGGAGTGAGTGCCCCTCCTCCTCCTCTTCGTGCTCCTCTCTGCTTCTCCTCCCCTCGCGCTCCTAGCAA[A/G]
TAGGAGTAGTACTCGAGCTTGCGCGATCTGTGTGGGAGAGGGGAGGTCGTGGCTTCTCTGATTCGGGCGGTTGGGGCGAGTCAAATGCGGTTGCTTGGTG

Reverse complement sequence

CACCAAGCAACCGCATTTGACTCGCCCCAACCGCCCGAATCAGAGAAGCCACGACCTCCCCTCTCCCACACAGATCGCGCAAGCTCGAGTACTACTCCTA[T/C]
TTGCTAGGAGCGCGAGGGGAGGAGAAGCAGAGAGGAGCACGAAGAGGAGGAGGAGGGGCACTCACTCCTGGGCACGAGCGCCGGCGGCGACAGCCTCGCC

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	80.80%	19.20%	0.02%	0.00%	NA
All Indica	2759	99.20%	0.70%	0.04%	0.00%	NA
All Japonica	1512	46.50%	53.50%	0.00%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.90%	0.13%	0.00%	NA
Temperate Japonica	767	33.10%	66.90%	0.00%	0.00%	NA
Tropical Japonica	504	72.40%	27.60%	0.00%	0.00%	NA
Japonica Intermediate	241	34.90%	65.10%	0.00%	0.00%	NA
VI/Aromatic	96	47.90%	52.10%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	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
vg0103512299	A -> G	LOC_Os01g07400.1	downstream_gene_variant ; 1768.0bp to feature; MODIFIER	silent_mutation	Average:88.945; most accessible tissue: Zhenshan97 flower, score: 93.851	N	N	N	N
vg0103512299	A -> G	LOC_Os01g07420.1	downstream_gene_variant ; 4359.0bp to feature; MODIFIER	silent_mutation	Average:88.945; most accessible tissue: Zhenshan97 flower, score: 93.851	N	N	N	N
vg0103512299	A -> G	LOC_Os01g07400.2	downstream_gene_variant ; 1768.0bp to feature; MODIFIER	silent_mutation	Average:88.945; most accessible tissue: Zhenshan97 flower, score: 93.851	N	N	N	N
vg0103512299	A -> G	LOC_Os01g07410.1	intron_variant ; MODIFIER	silent_mutation	Average:88.945; most accessible tissue: Zhenshan97 flower, score: 93.851	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)
vg0103512299	A	G	0.02	0.01	0.0	0.02	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103512299	NA	9.88E-07	mr1070	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
vg0103512299	5.89E-06	NA	mr1092	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
vg0103512299	NA	2.20E-10	mr1092	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
vg0103512299	NA	9.56E-07	mr1097	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
vg0103512299	7.48E-06	7.48E-06	mr1122	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
vg0103512299	1.12E-06	1.12E-06	mr1130	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
vg0103512299	NA	8.60E-08	mr1152	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
vg0103512299	NA	6.68E-09	mr1154	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
vg0103512299	NA	5.41E-07	mr1252	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
vg0103512299	NA	4.23E-06	mr1482	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
vg0103512299	NA	1.64E-06	mr1889	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
vg0103512299	NA	2.11E-06	mr1097_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
vg0103512299	NA	4.11E-07	mr1568_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
vg0103512299	NA	7.63E-06	mr1768_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