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Detailed information for vg1016429377:

Variant ID: vg1016429377 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16429377
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAACAACAGGCTATATTGTAGCTAGCTGATAGAGGAAATGAGCTTAGTGGTGTCCGTTGCCTCCGCCAGAGCCAGAGCCATATCCAGAGCCAGAGCCAGA[G/A]
CCGGAGCCTCCACCTTGGCCTCCACCGCCACCGCCACCGCCACCACTTCCATAACCACCACCATGAGCACCACCAGCACCCGACCCATAGCCGGAACCAT

Reverse complement sequence

ATGGTTCCGGCTATGGGTCGGGTGCTGGTGGTGCTCATGGTGGTGGTTATGGAAGTGGTGGCGGTGGCGGTGGCGGTGGAGGCCAAGGTGGAGGCTCCGG[C/T]
TCTGGCTCTGGCTCTGGATATGGCTCTGGCTCTGGCGGAGGCAACGGACACCACTAAGCTCATTTCCTCTATCAGCTAGCTACAATATAGCCTGTTGTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.80%	49.10%	0.06%	0.00%	NA
All Indica	2759	82.90%	17.10%	0.04%	0.00%	NA
All Japonica	1512	4.60%	95.40%	0.00%	0.00%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	73.40%	26.40%	0.17%	0.00%	NA
Indica II	465	92.70%	7.30%	0.00%	0.00%	NA
Indica III	913	84.10%	15.90%	0.00%	0.00%	NA
Indica Intermediate	786	82.80%	17.20%	0.00%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	13.70%	86.30%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	38.90%	58.90%	2.22%	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
vg1016429377	G -> A	LOC_Os10g31330.1	synonymous_variant ; p.Gly196Gly; LOW	synonymous_codon	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	N	N	N	N
vg1016429377	G -> A	LOC_Os10g31330.1	synonymous_variant ; p.Gly196Gly; LOW	nonsynonymous_codon ; G196S	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	unknown	unknown	DELETERIOUS	0.03
vg1016429377	G -> A	LOC_Os10g31330.2	synonymous_variant ; p.Gly183Gly; LOW	synonymous_codon	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	N	N	N	N
vg1016429377	G -> A	LOC_Os10g31330.2	synonymous_variant ; p.Gly183Gly; LOW	nonsynonymous_codon ; G183S	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	unknown	unknown	DELETERIOUS	0.02
vg1016429377	G -> A	LOC_Os10g31330.5	synonymous_variant ; p.Gly180Gly; LOW	synonymous_codon	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	N	N	N	N
vg1016429377	G -> A	LOC_Os10g31330.5	synonymous_variant ; p.Gly180Gly; LOW	nonsynonymous_codon ; G180S	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	unknown	unknown	DELETERIOUS	0.03
vg1016429377	G -> A	LOC_Os10g31330.6	synonymous_variant ; p.Gly174Gly; LOW	synonymous_codon	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	N	N	N	N
vg1016429377	G -> A	LOC_Os10g31330.6	synonymous_variant ; p.Gly174Gly; LOW	nonsynonymous_codon ; G174S	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	unknown	unknown	DELETERIOUS	0.03
vg1016429377	G -> A	LOC_Os10g31330.3	non_coding_transcript_variant ; MODIFIER	synonymous_codon	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	N	N	N	N
vg1016429377	G -> A	LOC_Os10g31330.3	non_coding_transcript_variant ; MODIFIER	nonsynonymous_codon ; G157S	Average:88.18; most accessible tissue: Minghui63 flower, score: 93.6	unknown	unknown	TOLERATED	0.06

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)
vg1016429377	G	A	-0.04	-0.05	-0.06	-0.04	-0.03	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016429377	NA	7.23E-12	mr1316	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
vg1016429377	NA	2.28E-07	mr1716	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
vg1016429377	NA	1.24E-06	mr1761	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
vg1016429377	4.09E-06	4.48E-09	mr1864_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
vg1016429377	3.65E-06	3.65E-06	mr1984_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