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Detailed information for vg1008185143:

Variant ID: vg1008185143 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8185143
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.25, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

CTAAAGTCCTCCCTGTCCGGATATGCAGTAGAATGACATCTGTGAGCAGCGGGCTGGCCAGTGCCTGAAGTATCGTGTTAGAATTAAACTGAGCATTCCG[T/C]
AGACACTCTTTCTCACTAGGAAATCCTCTCTACCCTTTGCCTAATTTGCTTCGTGTCCTTGGATGAGCCGGAAGAGGAGCTGAACACACACGTTCCCTGA

Reverse complement sequence

TCAGGGAACGTGTGTGTTCAGCTCCTCTTCCGGCTCATCCAAGGACACGAAGCAAATTAGGCAAAGGGTAGAGAGGATTTCCTAGTGAGAAAGAGTGTCT[A/G]
CGGAATGCTCAGTTTAATTCTAACACGATACTTCAGGCACTGGCCAGCCCGCTGCTCACAGATGTCATTCTACTGCATATCCGGACAGGGAGGACTTTAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.30%	16.00%	0.40%	3.28%	NA
All Indica	2759	98.90%	0.90%	0.04%	0.07%	NA
All Japonica	1512	43.20%	46.70%	0.26%	9.85%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.00%	0.22%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.40%	0.13%	0.13%	NA
Temperate Japonica	767	12.90%	67.50%	0.39%	19.17%	NA
Tropical Japonica	504	89.90%	9.90%	0.20%	0.00%	NA
Japonica Intermediate	241	41.90%	57.30%	0.00%	0.83%	NA
VI/Aromatic	96	78.10%	8.30%	13.54%	0.00%	NA
Intermediate	90	76.70%	17.80%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1008185143	T -> C	LOC_Os10g16410.1	downstream_gene_variant ; 4208.0bp to feature; MODIFIER	silent_mutation	Average:66.018; most accessible tissue: Minghui63 flag leaf, score: 85.327	N	N	N	N
vg1008185143	T -> C	LOC_Os10g16410-LOC_Os10g16430	intergenic_region ; MODIFIER	silent_mutation	Average:66.018; most accessible tissue: Minghui63 flag leaf, score: 85.327	N	N	N	N
vg1008185143	T -> DEL	N	N	silent_mutation	Average:66.018; most accessible tissue: Minghui63 flag leaf, score: 85.327	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)
vg1008185143	T	C	0.0	0.0	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008185143	NA	2.73E-09	mr1624	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
vg1008185143	NA	2.06E-24	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
vg1008185143	NA	3.52E-09	mr1679	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
vg1008185143	NA	1.28E-10	mr1691	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
vg1008185143	NA	2.03E-10	mr1693	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
vg1008185143	NA	7.19E-07	mr1495_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
vg1008185143	4.83E-06	NA	mr1519_2	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
vg1008185143	NA	3.07E-09	mr1624_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
vg1008185143	NA	4.50E-23	mr1679_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
vg1008185143	NA	1.16E-07	mr1691_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
vg1008185143	NA	2.31E-07	mr1733_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