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Detailed information for vg0609338220:

Variant ID: vg0609338220 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 9338220
Reference Allele: CAAGA	Alternative Allele: C
Primary Allele: CAAGA	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTCCCTTCACTTCAGCTCCATGGACAGGGAGGCCAGGGTGCTCAGGTACAGGGAGAAGAAGAAGGCCAGGAAGTTTGAGAAGACAATACGTTATGAAA[CAAGA/C]
AAGGCGTATGCAGAGGCACGACCCCGGATCAAGGGCCGTTTCGCCAAGAGATCAGATGTGCAGATCGAAGTGGACCAGATGTTCTCCACTGCAGCTCTAT

Reverse complement sequence

ATAGAGCTGCAGTGGAGAACATCTGGTCCACTTCGATCTGCACATCTGATCTCTTGGCGAAACGGCCCTTGATCCGGGGTCGTGCCTCTGCATACGCCTT[TCTTG/G]
TTTCATAACGTATTGTCTTCTCAAACTTCCTGGCCTTCTTCTTCTCCCTGTACCTGAGCACCCTGGCCTCCCTGTCCATGGAGCTGAAGTGAAGGGACAT

Allele Frequencies:

Populations	Population Size	Frequency of CAAGA(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.30%	15.20%	2.52%	0.00%	NA
All Indica	2759	70.60%	25.10%	4.28%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	73.30%	16.80%	9.92%	0.00%	NA
Indica II	465	21.50%	71.20%	7.31%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	67.40%	29.40%	3.18%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	0.00%	NA

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

Category	Variant ID	Chrom	Pos	Gene	MSU	RAP	Alt_Allele_Function	Ref_geno	Alt_geno
Heading date	vg0609338220	Chr6	9338220	Hd1	LOC_Os06g16370	Os06g0275000	promoting heading date under LD	CAAGA	C

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609338220	CAAGA -> C	LOC_Os06g16370.1	frameshift_variant ; p.Lys352fs; HIGH	frameshift_variant	Average:81.098; most accessible tissue: Zhenshan97 panicle, score: 93.455	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)
vg0609338220	CAAGA	C	-0.05	0.15	0.1	0.14	0.27	0.35