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Detailed information for vg1105172102:

Variant ID: vg1105172102 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5172102
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGAGGGGAGGAAAGGGTGGGATGCTGTGCTGGGTGGAGAAGACGGAGAGTTTGTAGTCAGTTTCTATCTCTACTGAGGTGAGTCATGACTGGGGAGAGC[C/A]
TGGGAGTCAGTTTGCTGTGCATATAGTTTTATTTTATTTTTTTGTTACTAGCATGAAAATAAAGTTAGGACGCGGGAAAAAATATTACCGCATTATTAAT

Reverse complement sequence

ATTAATAATGCGGTAATATTTTTTCCCGCGTCCTAACTTTATTTTCATGCTAGTAACAAAAAAATAAAATAAAACTATATGCACAGCAAACTGACTCCCA[G/T]
GCTCTCCCCAGTCATGACTCACCTCAGTAGAGATAGAAACTGACTACAAACTCTCCGTCTTCTCCACCCAGCACAGCATCCCACCCTTTCCTCCCCTCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	27.20%	0.32%	6.22%	NA
All Indica	2759	84.00%	8.70%	0.29%	7.00%	NA
All Japonica	1512	38.20%	61.30%	0.40%	0.13%	NA
Aus	269	55.40%	10.00%	0.00%	34.57%	NA
Indica I	595	70.40%	4.70%	0.34%	24.54%	NA
Indica II	465	96.10%	3.20%	0.43%	0.22%	NA
Indica III	913	91.70%	7.20%	0.11%	0.99%	NA
Indica Intermediate	786	78.20%	16.70%	0.38%	4.71%	NA
Temperate Japonica	767	36.50%	63.10%	0.39%	0.00%	NA
Tropical Japonica	504	36.10%	63.10%	0.40%	0.40%	NA
Japonica Intermediate	241	47.70%	51.90%	0.41%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	67.80%	24.40%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105172102	C -> A	LOC_Os11g09684.1	3_prime_UTR_variant ; 24.0bp to feature; MODIFIER	silent_mutation	Average:90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773	N	N	N	N
vg1105172102	C -> A	LOC_Os11g09680.1	upstream_gene_variant ; 879.0bp to feature; MODIFIER	silent_mutation	Average:90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773	N	N	N	N
vg1105172102	C -> A	LOC_Os11g09680.2	upstream_gene_variant ; 879.0bp to feature; MODIFIER	silent_mutation	Average:90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773	N	N	N	N
vg1105172102	C -> A	LOC_Os11g09690.1	downstream_gene_variant ; 1412.0bp to feature; MODIFIER	silent_mutation	Average:90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773	N	N	N	N
vg1105172102	C -> DEL	N	N	silent_mutation	Average:90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773	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)
vg1105172102	C	A	-0.01	-0.03	-0.04	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105172102	NA	8.43E-06	mr1128_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
vg1105172102	NA	9.78E-06	mr1204_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
vg1105172102	NA	2.39E-07	mr1376_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
vg1105172102	NA	1.29E-07	mr1431_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
vg1105172102	NA	7.10E-06	mr1538_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
vg1105172102	NA	1.63E-06	mr1594_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
vg1105172102	NA	7.50E-07	mr1624_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
vg1105172102	NA	2.43E-08	mr1758_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