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Detailed information for vg0724226199:

Variant ID: vg0724226199 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 24226199
Reference Allele: TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC	Alternative Allele: CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC,T
Primary Allele: TGTGAGGTCCCCTTAACTGT ATAAAACCAGTCAC	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGGGACAATGAAACGTCTTCGAACCATAAAACTAGATATGTGAGGTCCCCTTAACTGTATAAAACCGGTCACCCGAAATCAAGACCGTAAAACTAGATA[TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC/CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC,T]
CCGAGATCCTTCAGTGGTTTTGACCCCGATTTTAGTCTACATGGCAGCTGAGCCAGCATGGGACCCACATGAGCCCCACATGTCAGCGGGCCACGTCAAC

Reverse complement sequence

GTTGACGTGGCCCGCTGACATGTGGGGCTCATGTGGGTCCCATGCTGGCTCAGCTGCCATGTAGACTAAAATCGGGGTCAAAACCACTGAAGGATCTCGG[GTGACTGGTTTTATACAGTTAAGGGGACCTCACA/GTGACTGGTTTTATACAGTTAAGGGGACCTCACG,A]
TATCTAGTTTTACGGTCTTGATTTCGGGTGACCGGTTTTATACAGTTAAGGGGACCTCACATATCTAGTTTTATGGTTCGAAGACGTTTCATTGTCCCGA

Allele Frequencies:

Populations	Population Size	Frequency of TGTGAGGTCCCCTTAACTGT ATAAAACCAGTCAC(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.50%	9.80%	0.55%	1.23%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 4.93%
All Indica	2759	81.40%	16.00%	0.43%	1.27%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 0.87%
All Japonica	1512	95.80%	0.10%	0.73%	1.52%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 1.79%
Aus	269	32.00%	0.00%	1.12%	0.00%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 66.91%
Indica I	595	97.60%	1.00%	0.17%	1.01%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 0.17%
Indica II	465	85.80%	14.20%	0.00%	0.00%	NA
Indica III	913	70.80%	28.40%	0.22%	0.11%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 0.55%
Indica Intermediate	786	78.90%	14.10%	1.15%	3.56%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 2.29%
Temperate Japonica	767	96.00%	0.00%	0.91%	0.26%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 2.87%
Tropical Japonica	504	98.40%	0.20%	0.00%	1.39%	NA
Japonica Intermediate	241	90.00%	0.40%	1.66%	5.81%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 2.07%
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	0.00%	0.00%	CGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724226199	TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC -> DEL	N	N	silent_mutation	Average:67.914; most accessible tissue: Zhenshan97 panicle, score: 91.03	N	N	N	N
vg0724226199	TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC -> CGTGAGGTCCCCTTAACTGTATAAAACCAG TCAC	LOC_Os07g40420.1	downstream_gene_variant ; 3170.0bp to feature; MODIFIER	silent_mutation	Average:67.914; most accessible tissue: Zhenshan97 panicle, score: 91.03	N	N	N	N
vg0724226199	TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC -> CGTGAGGTCCCCTTAACTGTATAAAACCAG TCAC	LOC_Os07g40404.1	intron_variant ; MODIFIER	silent_mutation	Average:67.914; most accessible tissue: Zhenshan97 panicle, score: 91.03	N	N	N	N
vg0724226199	TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC -> T	LOC_Os07g40420.1	downstream_gene_variant ; 3169.0bp to feature; MODIFIER	silent_mutation	Average:67.914; most accessible tissue: Zhenshan97 panicle, score: 91.03	N	N	N	N
vg0724226199	TGTGAGGTCCCCTTAACTGTATAAAACCAGTCAC -> T	LOC_Os07g40404.1	intron_variant ; MODIFIER	silent_mutation	Average:67.914; most accessible tissue: Zhenshan97 panicle, score: 91.03	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)
vg0724226199	TGTGA*	CGTGA*	0.09	0.07	0.04	0.07	0.06	0.04
vg0724226199	TGTGA*	T	0.57	0.53	0.36	0.28	0.35	0.36

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724226199	3.24E-06	NA	mr1354	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
vg0724226199	NA	1.49E-37	mr1549	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
vg0724226199	NA	3.41E-46	mr1550	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
vg0724226199	3.25E-06	NA	mr1829	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
vg0724226199	NA	1.36E-11	mr1409_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
vg0724226199	NA	3.55E-30	mr1549_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
vg0724226199	NA	1.64E-53	mr1550_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
vg0724226199	NA	1.41E-27	mr1757_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
vg0724226199	3.56E-12	NA	mr1829_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
vg0724226199	4.77E-11	NA	mr1842_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