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Detailed information for vg0529385032:

Variant ID: vg0529385032 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29385032
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.36, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGATTTTCTCGTAACTATTTTGATCATCTACAAGAAACAGCACACTCCATTAACAGTACAAAACATTTTCCCTATAGAGCATCTTTACTATCTTTGA[A/G]
AAGGTACCATGAGGTAGCAATATAATCTAACCGTTGGTTTAGAAATGGGTATGATCGGGCTAAAGAAATTACCGTCGTTGCATCAAGGCTGTCGTGGCTG

Reverse complement sequence

CAGCCACGACAGCCTTGATGCAACGACGGTAATTTCTTTAGCCCGATCATACCCATTTCTAAACCAACGGTTAGATTATATTGCTACCTCATGGTACCTT[T/C]
TCAAAGATAGTAAAGATGCTCTATAGGGAAAATGTTTTGTACTGTTAATGGAGTGTGCTGTTTCTTGTAGATGATCAAAATAGTTACGAGAAAATCTGAA

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	64.10%	35.60%	0.11%	0.21%	NA
All Indica	2759	95.10%	4.50%	0.11%	0.25%	NA
All Japonica	1512	4.80%	95.00%	0.00%	0.20%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	98.30%	1.20%	0.17%	0.34%	NA
Indica II	465	83.40%	15.70%	0.00%	0.86%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	5.00%	0.25%	0.13%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	13.10%	86.70%	0.00%	0.20%	NA
Japonica Intermediate	241	1.70%	97.50%	0.00%	0.83%	NA
VI/Aromatic	96	16.70%	82.30%	1.04%	0.00%	NA
Intermediate	90	56.70%	42.20%	1.11%	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
vg0529385032	A -> DEL	N	N	silent_mutation	Average:78.07; most accessible tissue: Zhenshan97 flag leaf, score: 97.97	N	N	N	N
vg0529385032	A -> G	LOC_Os05g51220.1	upstream_gene_variant ; 3533.0bp to feature; MODIFIER	silent_mutation	Average:78.07; most accessible tissue: Zhenshan97 flag leaf, score: 97.97	N	N	N	N
vg0529385032	A -> G	LOC_Os05g51230.1	downstream_gene_variant ; 494.0bp to feature; MODIFIER	silent_mutation	Average:78.07; most accessible tissue: Zhenshan97 flag leaf, score: 97.97	N	N	N	N
vg0529385032	A -> G	LOC_Os05g51240.1	downstream_gene_variant ; 884.0bp to feature; MODIFIER	silent_mutation	Average:78.07; most accessible tissue: Zhenshan97 flag leaf, score: 97.97	N	N	N	N
vg0529385032	A -> G	LOC_Os05g51230-LOC_Os05g51240	intergenic_region ; MODIFIER	silent_mutation	Average:78.07; most accessible tissue: Zhenshan97 flag leaf, score: 97.97	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)
vg0529385032	A	G	0.01	0.01	0.03	-0.02	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529385032	NA	1.05E-08	mr1275	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
vg0529385032	NA	1.86E-10	mr1325	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
vg0529385032	NA	1.61E-06	mr1425	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
vg0529385032	NA	1.05E-07	mr1439	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
vg0529385032	NA	1.31E-06	mr1532	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
vg0529385032	NA	8.35E-09	mr1575	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
vg0529385032	NA	1.72E-11	mr1623	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
vg0529385032	2.74E-06	2.74E-06	mr1623	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
vg0529385032	NA	1.25E-08	mr1986	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
vg0529385032	NA	1.57E-14	mr1162_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
vg0529385032	NA	1.39E-27	mr1588_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
vg0529385032	NA	3.05E-07	mr1588_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
vg0529385032	NA	3.58E-10	mr1595_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
vg0529385032	NA	2.09E-07	mr1749_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
vg0529385032	NA	1.26E-07	mr1821_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
vg0529385032	NA	1.59E-10	mr1893_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