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Detailed information for vg0135190066:

Variant ID: vg0135190066 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 35190066
Reference Allele: G	Alternative Allele: GCGGTCAGACCGGCCACTACACTA
Primary Allele: G	Secondary Allele: GCGGTCAGACCGGCCACTAC ACTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTTATGGTGGTGATACAGAGCTGCCAGAGCCGCAACCGGTCAGACCGAGCCGAAGGAGGTCTGACCGAGCCGTGGACGGTCTGACCGGCCACTACACT[G/GCGGTCAGACCGGCCACTACACTA]
CGGTCAGACCGGCCAGGTTGAGTGGGCTCAATGACTGCCAACTAGCCGTTACAAAGTAGTCCGGTCTGACCGGCCACTCTATGGCGGTCGGACCGGCAGA

Reverse complement sequence

TCTGCCGGTCCGACCGCCATAGAGTGGCCGGTCAGACCGGACTACTTTGTAACGGCTAGTTGGCAGTCATTGAGCCCACTCAACCTGGCCGGTCTGACCG[C/TAGTGTAGTGGCCGGTCTGACCGC]
AGTGTAGTGGCCGGTCAGACCGTCCACGGCTCGGTCAGACCTCCTTCGGCTCGGTCTGACCGGTTGCGGCTCTGGCAGCTCTGTATCACCACCATAAACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of GCGGTCAGACCGGCCACTAC ACTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.20%	0.90%	0.87%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	95.20%	2.40%	2.45%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	89.50%	6.00%	4.56%	0.00%	NA
Japonica Intermediate	241	92.10%	2.50%	5.39%	0.00%	NA
VI/Aromatic	96	90.60%	6.20%	3.12%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0135190066	G -> GCGGTCAGACCGGCCACTACACTA	LOC_Os01g60860.1	upstream_gene_variant ; 2063.0bp to feature; MODIFIER	silent_mutation	Average:71.894; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0135190066	G -> GCGGTCAGACCGGCCACTACACTA	LOC_Os01g60870.1	upstream_gene_variant ; 2396.0bp to feature; MODIFIER	silent_mutation	Average:71.894; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0135190066	G -> GCGGTCAGACCGGCCACTACACTA	LOC_Os01g60860-LOC_Os01g60870	intergenic_region ; MODIFIER	silent_mutation	Average:71.894; most accessible tissue: Zhenshan97 panicle, score: 86.058	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)
vg0135190066	G	GCGGT*	0.09	0.13	0.08	0.04	0.08	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135190066	6.75E-06	6.75E-06	mr1312_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
vg0135190066	NA	2.04E-06	mr1397_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
vg0135190066	8.61E-07	8.61E-07	mr1427_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
vg0135190066	7.16E-06	7.16E-06	mr1663_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
vg0135190066	5.89E-06	NA	mr1665_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
vg0135190066	3.76E-06	3.75E-06	mr1847_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