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Detailed information for vg1101470341:

Variant ID: vg1101470341 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 1470341
Reference Allele: A	Alternative Allele: ACCCAGCCGGCCCT,ACCCAGCCGGCCCTCC,ACC,ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC,ACCCAGCCGGCCCTCCCCGACGCTCCCCT,ACCCAGCCGGCCCTCCCCGACGCTCCC
Primary Allele: A	Secondary Allele: ACC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCCGCCCTGTCGTCCTCGCCACCCTGTCCTCCTCCCCCTGTCGTCCCCGCGGTCCGTCGCCGCCACCGCCACCGCCGCCTGGCGAGTCATCCTGTGCT[A/ACCCAGCCGGCCCT,ACCCAGCCGGCCCTCC,ACC,ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC,ACCCAGCCGGCCCTCCCCGACGCTCCCCT,ACCCAGCCGGCCCTCCCCGACGCTCCC]
CACGGACATTTTGGGCATAAAAGTCTCCAAAGTGGCATTTCATCCGGTAAACAATGTATTGAGTGGCATTTTATCTGGTGCATTATATTGAGTGGCATTT

Reverse complement sequence

AAATGCCACTCAATATAATGCACCAGATAAAATGCCACTCAATACATTGTTTACCGGATGAAATGCCACTTTGGAGACTTTTATGCCCAAAATGTCCGTG[T/AGGGCCGGCTGGGT,GGAGGGCCGGCTGGGT,GGT,GAGAGAGAGGAGAGGGGAGCGTCGGGGAGGGCCGGCTGGGT,AGGGGAGCGTCGGGGAGGGCCGGCTGGGT,GGGAGCGTCGGGGAGGGCCGGCTGGGT]
AGCACAGGATGACTCGCCAGGCGGCGGTGGCGGTGGCGGCGACGGACCGCGGGGACGACAGGGGGAGGAGGACAGGGTGGCGAGGACGACAGGGCGGAGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of ACC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.20%	0.40%	18.54%	34.30%	ACCCAGCCGGCCCTCC: 0.15%; ACCCAGCCGGCCCT: 0.15%; ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.13%; ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC: 0.08%; ACCCAGCCGGCCCTCCCCGACGCTCCC: 0.08%
All Indica	2759	23.70%	0.40%	25.41%	49.76%	ACCCAGCCGGCCCTCC: 0.22%; ACCCAGCCGGCCCT: 0.18%; ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.18%; ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC: 0.11%; ACCCAGCCGGCCCTCCCCGACGCTCCC: 0.04%
All Japonica	1512	85.50%	0.20%	5.89%	8.40%	NA
Aus	269	34.90%	1.10%	27.14%	34.94%	ACCCAGCCGGCCCTCCCCGACGCTCCC: 1.12%; ACCCAGCCGGCCCT: 0.74%
Indica I	595	15.50%	0.20%	42.18%	41.85%	ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.17%; ACCCAGCCGGCCCTCC: 0.17%
Indica II	465	27.50%	0.00%	29.46%	41.94%	ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC: 0.43%; ACCCAGCCGGCCCTCCCCGACGCTCCC: 0.22%; ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.22%; ACCCAGCCGGCCCT: 0.22%
Indica III	913	26.30%	0.70%	11.06%	61.34%	ACCCAGCCGGCCCT: 0.33%; ACCCAGCCGGCCCTCC: 0.22%; ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.11%
Indica Intermediate	786	24.70%	0.50%	26.97%	46.95%	ACCCAGCCGGCCCTCC: 0.38%; ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 0.25%; ACCCAGCCGGCCCT: 0.13%; ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC: 0.13%
Temperate Japonica	767	94.50%	0.00%	3.26%	2.22%	NA
Tropical Japonica	504	71.80%	0.60%	9.72%	17.86%	NA
Japonica Intermediate	241	85.50%	0.00%	6.22%	8.30%	NA
VI/Aromatic	96	91.70%	0.00%	3.12%	5.21%	NA
Intermediate	90	60.00%	1.10%	11.11%	24.44%	ACCCAGCCGGCCCTCCCCGACGCTCCCCT: 1.11%; ACCCAGCCGGCCCTCC: 1.11%; ACCCAGCCGGCCCTCCCCGACGCTCCCCTCTCCTCTCTCTC: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCT	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCT	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCT	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCT	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCT	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> DEL	N	N	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCTC TCCTCTCTCTC	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCTC TCCTCTCTCTC	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCTC TCCTCTCTCTC	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCTC TCCTCTCTCTC	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCCCTC TCCTCTCTCTC	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCC	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCC	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCC	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCC	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCC	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACC	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACC	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACC	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACC	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACC	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCC	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCC	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCC	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCC	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCTCCCCGACGCTCCC	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCT	LOC_Os11g03740.1	upstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCT	LOC_Os11g03734.1	downstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCT	LOC_Os11g03750.1	downstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCT	LOC_Os11g03760.1	downstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	N	N	N	N
vg1101470341	A -> ACCCAGCCGGCCCT	LOC_Os11g03740-LOC_Os11g03750	intergenic_region ; MODIFIER	silent_mutation	Average:83.709; most accessible tissue: Zhenshan97 panicle, score: 94.88	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)
vg1101470341	A	ACC	-0.27	-0.22	-0.23	-0.18	-0.22	-0.21
vg1101470341	A	ACCCA*	0.06	0.07	0.03	0.08	0.07	0.08

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101470341	3.58E-07	NA	mr1623	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
vg1101470341	NA	2.09E-11	mr1630	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
vg1101470341	NA	8.72E-07	mr1785	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