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Detailed information for vg1123431948:

Variant ID: vg1123431948 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 23431948
Reference Allele: CTG	Alternative Allele: ATG,C
Primary Allele: CTG	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACATTGCCTTCCAGCATCTGCACAACCTCTGACATAGCAGGGCGAAGATGAGGCTCCACATGAGTGCAGAGGAGTGCTATTTGGATCATCTTCTCCAG[CTG/ATG,C]
TTGCAAATCGTATGCAGTGTCCAGGTTGTGGTCCACAATGTCTGTCAATCGTCCTCCTTGCACCAACCTTTTCACCTTCACATGTACCAAAGAGTCAATC

Reverse complement sequence

GATTGACTCTTTGGTACATGTGAAGGTGAAAAGGTTGGTGCAAGGAGGACGATTGACAGACATTGTGGACCACAACCTGGACACTGCATACGATTTGCAA[CAG/CAT,G]
CTGGAGAAGATGATCCAAATAGCACTCCTCTGCACTCATGTGGAGCCTCATCTTCGCCCTGCTATGTCAGAGGTTGTGCAGATGCTGGAAGGCAATGTTG

Allele Frequencies:

Populations	Population Size	Frequency of CTG(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.50%	9.50%	0.08%	0.00%	ATG: 6.92%
All Indica	2759	90.50%	5.00%	0.04%	0.00%	ATG: 4.49%
All Japonica	1512	76.10%	14.30%	0.13%	0.00%	ATG: 9.52%
Aus	269	74.30%	9.70%	0.00%	0.00%	ATG: 15.99%
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	94.40%	3.70%	0.00%	0.00%	ATG: 1.94%
Indica III	913	79.70%	9.10%	0.00%	0.00%	ATG: 11.17%
Indica Intermediate	786	94.10%	4.10%	0.13%	0.00%	ATG: 1.65%
Temperate Japonica	767	69.60%	14.70%	0.26%	0.00%	ATG: 15.38%
Tropical Japonica	504	86.50%	13.50%	0.00%	0.00%	NA
Japonica Intermediate	241	74.70%	14.50%	0.00%	0.00%	ATG: 10.79%
VI/Aromatic	96	28.10%	63.50%	0.00%	0.00%	ATG: 8.33%
Intermediate	90	77.80%	12.20%	1.11%	0.00%	ATG: 8.89%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123431948	CTG -> ATG	LOC_Os11g39370.1	missense_variant ; p.Gln527His; MODERATE	nonsynonymous_codon ; Q527D	Average:69.269; most accessible tissue: Zhenshan97 young leaf, score: 86.055	benign	-0.283	N	N
vg1123431948	CTG -> ATG	LOC_Os11g39370.1	missense_variant ; p.Gln527His; MODERATE	nonsynonymous_codon ; Q527H	Average:69.269; most accessible tissue: Zhenshan97 young leaf, score: 86.055	possibly damaging	+1.919	N	N
vg1123431948	CTG -> C	LOC_Os11g39370.1	frameshift_variant ; p.Gln527fs; HIGH	frameshift_variant	Average:69.269; most accessible tissue: Zhenshan97 young leaf, score: 86.055	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)
vg1123431948	CTG	ATG	0.0	-0.01	-0.01	0.0	0.0	0.01
vg1123431948	CTG	C	-0.06	-0.01	-0.11	0.07	0.01	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123431948	3.38E-10	8.50E-07	Awn_length	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652