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Detailed information for vg0138183041:

Variant ID: vg0138183041 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 38183041
Reference Allele: CAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT	Alternative Allele: TAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT,C
Primary Allele: CAAATTTTGATAAGGTTGTT AAAATTTTAGTAAGGTTATT	Secondary Allele: TAAATTTTGATAAGGTTGTT AAAATTTTAGTAAGGTTATT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGACGAACAACGACGGTGATTGTGCTGCGTTAGCCGTTAGTCACTGAAGGACTTGTTCATTTTGCTACTATTTTCAATCTTAATAAGTTTTGACATTGT[CAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT/TAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT,C]
AAATTTTGGAGATTTTATATGTGCTTACTAAAATTTAGCAACAAACCATATAGCCACTTTTTTAAAACTTTGAAAAAAAAAGTATTTTTGAAAATGGTAG

Reverse complement sequence

CTACCATTTTCAAAAATACTTTTTTTTTCAAAGTTTTAAAAAAGTGGCTATATGGTTTGTTGCTAAATTTTAGTAAGCACATATAAAATCTCCAAAATTT[AATAACCTTACTAAAATTTTAACAACCTTATCAAAATTTG/AATAACCTTACTAAAATTTTAACAACCTTATCAAAATTTA,G]
ACAATGTCAAAACTTATTAAGATTGAAAATAGTAGCAAAATGAACAAGTCCTTCAGTGACTAACGGCTAACGCAGCACAATCACCGTCGTTGTTCGTCAT

Allele Frequencies:

Populations	Population Size	Frequency of CAAATTTTGATAAGGTTGTT AAAATTTTAGTAAGGTTATT(primary allele)	Frequency of TAAATTTTGATAAGGTTGTT AAAATTTTAGTAAGGTTATT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	6.10%	1.04%	0.00%	C: 0.06%
All Indica	2759	98.00%	1.60%	0.29%	0.00%	C: 0.07%
All Japonica	1512	86.40%	11.30%	2.25%	0.00%	C: 0.07%
Aus	269	72.90%	25.30%	1.86%	0.00%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	99.40%	0.20%	0.22%	0.00%	C: 0.22%
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.10%	0.25%	0.00%	C: 0.13%
Temperate Japonica	767	96.60%	0.50%	2.74%	0.00%	C: 0.13%
Tropical Japonica	504	66.70%	31.20%	2.18%	0.00%	NA
Japonica Intermediate	241	95.00%	4.10%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	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
vg0138183041	CAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT -> C	LOC_Os01g65760-LOC_Os01g65770	intergenic_region ; MODIFIER	silent_mutation	Average:91.7; most accessible tissue: Minghui63 flower, score: 97.106	N	N	N	N
vg0138183041	CAAATTTTGATAAGGTTGTTAAAATTTTAGTAAGGTTATT -> TAAATTTTGATAAGGTTGTTAAAATTTTAG TAAGGTTATT	LOC_Os01g65760-LOC_Os01g65770	intergenic_region ; MODIFIER	silent_mutation	Average:91.7; most accessible tissue: Minghui63 flower, score: 97.106	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)
vg0138183041	CAAAT*	C	0.33	0.3	0.58	0.14	0.15	0.17
vg0138183041	CAAAT*	TAAAT*	0.0	0.01	0.0	0.02	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0138183041	5.91E-06	NA	mr1134	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
vg0138183041	1.62E-06	NA	mr1135	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
vg0138183041	1.24E-06	NA	mr1504	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