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Detailed information for vg0134995977:

Variant ID: vg0134995977 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34995977
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTCCGTTGCTGCAATTTGCCAGTAAAAAAGCATGCCCGCATCGCACCCGGACGCTTACGTCAGTTCAAGAGCCTCACCAAGGTCGCAATAAACAAGAG[G/A]
CAAAACATATATAATACACTCATAGTAGTACTAGAGAAACTATCCTCAAAACTAAAAAAAAAACGATATGAGAAATTGTGCATGCATTGAGAGCAAGCTA

Reverse complement sequence

TAGCTTGCTCTCAATGCATGCACAATTTCTCATATCGTTTTTTTTTTAGTTTTGAGGATAGTTTCTCTAGTACTACTATGAGTGTATTATATATGTTTTG[C/T]
CTCTTGTTTATTGCGACCTTGGTGAGGCTCTTGAACTGACGTAAGCGTCCGGGTGCGATGCGGGCATGCTTTTTTACTGGCAAATTGCAGCAACGGACAC

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	89.40%	10.20%	0.04%	0.28%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	85.90%	13.10%	0.13%	0.86%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	93.90%	6.00%	0.13%	0.00%	NA
Tropical Japonica	504	88.70%	8.50%	0.20%	2.58%	NA
Japonica Intermediate	241	54.80%	45.20%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0134995977	G -> A	LOC_Os01g60520.1	upstream_gene_variant ; 815.0bp to feature; MODIFIER	silent_mutation	Average:52.719; most accessible tissue: Minghui63 root, score: 97.631	N	N	N	N
vg0134995977	G -> A	LOC_Os01g60510.1	downstream_gene_variant ; 1694.0bp to feature; MODIFIER	silent_mutation	Average:52.719; most accessible tissue: Minghui63 root, score: 97.631	N	N	N	N
vg0134995977	G -> A	LOC_Os01g60510-LOC_Os01g60520	intergenic_region ; MODIFIER	silent_mutation	Average:52.719; most accessible tissue: Minghui63 root, score: 97.631	N	N	N	N
vg0134995977	G -> DEL	N	N	silent_mutation	Average:52.719; most accessible tissue: Minghui63 root, score: 97.631	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)
vg0134995977	G	A	-0.02	0.02	0.01	0.01	0.04	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134995977	NA	2.16E-06	mr1113	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
vg0134995977	NA	9.31E-08	mr1117	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
vg0134995977	NA	1.91E-06	mr1118	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
vg0134995977	NA	3.60E-06	mr1123	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
vg0134995977	NA	2.71E-07	mr1240	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
vg0134995977	NA	8.71E-06	mr1242	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
vg0134995977	NA	5.95E-07	mr1496	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
vg0134995977	9.63E-06	NA	mr1679	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
vg0134995977	NA	4.78E-07	mr1691	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
vg0134995977	4.51E-07	NA	mr1693	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
vg0134995977	9.86E-06	9.30E-12	mr1693	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
vg0134995977	NA	3.04E-06	mr1917	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
vg0134995977	NA	5.46E-06	mr1117_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
vg0134995977	NA	9.05E-07	mr1496_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