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Detailed information for vg1124898092:

Variant ID: vg1124898092 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24898092
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGGGTCCCACAAAACGATCTGTACACTGTATAGATTGAACTGAAGCTTTGTTTCTTGGATGGACTGATCTGTACATTGTTGGACTGACATGTGGGGCC[C/T]
ACATGGGCCCCACCATTTTTTATTATTTTCTGTGTGAGACTGACATGTGGGTCCCACGAGTTTTATTATTTTTCAGGATCGAATTACCACGTAAGCGCCA

Reverse complement sequence

TGGCGCTTACGTGGTAATTCGATCCTGAAAAATAATAAAACTCGTGGGACCCACATGTCAGTCTCACACAGAAAATAATAAAAAATGGTGGGGCCCATGT[G/A]
GGCCCCACATGTCAGTCCAACAATGTACAGATCAGTCCATCCAAGAAACAAAGCTTCAGTTCAATCTATACAGTGTACAGATCGTTTTGTGGGACCCACT

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	96.70%	0.20%	0.59%	2.52%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.04%	NA
All Japonica	1512	90.10%	0.60%	1.79%	7.54%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.40%	0.30%	0.39%	3.91%	NA
Tropical Japonica	504	82.30%	0.80%	3.77%	13.10%	NA
Japonica Intermediate	241	89.20%	1.20%	2.07%	7.47%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124898092	C -> T	LOC_Os11g41500.1	upstream_gene_variant ; 4594.0bp to feature; MODIFIER	silent_mutation	Average:63.832; most accessible tissue: Minghui63 panicle, score: 92.928	N	N	N	N
vg1124898092	C -> T	LOC_Os11g41520.1	upstream_gene_variant ; 1875.0bp to feature; MODIFIER	silent_mutation	Average:63.832; most accessible tissue: Minghui63 panicle, score: 92.928	N	N	N	N
vg1124898092	C -> T	LOC_Os11g41510.1	downstream_gene_variant ; 509.0bp to feature; MODIFIER	silent_mutation	Average:63.832; most accessible tissue: Minghui63 panicle, score: 92.928	N	N	N	N
vg1124898092	C -> T	LOC_Os11g41500-LOC_Os11g41510	intergenic_region ; MODIFIER	silent_mutation	Average:63.832; most accessible tissue: Minghui63 panicle, score: 92.928	N	N	N	N
vg1124898092	C -> DEL	N	N	silent_mutation	Average:63.832; most accessible tissue: Minghui63 panicle, score: 92.928	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)
vg1124898092	C	T	-0.02	0.0	-0.02	0.07	0.06	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124898092	2.99E-07	2.33E-08	mr1238	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
vg1124898092	NA	6.77E-06	mr1484	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
vg1124898092	NA	6.61E-07	mr1900	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
vg1124898092	2.34E-09	5.84E-11	mr1238_2	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
vg1124898092	3.04E-08	3.04E-08	mr1484_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
vg1124898092	6.79E-06	6.79E-06	mr1609_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
vg1124898092	2.75E-06	4.68E-08	mr1841_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
vg1124898092	NA	5.94E-06	mr1866_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
vg1124898092	4.54E-07	2.64E-08	mr1900_2	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
vg1124898092	1.49E-09	1.49E-09	mr1945_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