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Detailed information for vg1112969673:

Variant ID: vg1112969673 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 12969673
Reference Allele: CGTTCTCT	Alternative Allele: TGTTCTCT,C
Primary Allele: CGTTCTCT	Secondary Allele: TGTTCTCT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGAATCGCCTTGTCCACCAACTGCTGGAAATCCCGTTATTCCATAGCCAGTAATGCATAAGACAACTCATCATTCAGTCCCTCTAAAAACTTCTCCTGA[CGTTCTCT/TGTTCTCT,C]
ATCAGTGCGAACATCCTCTGGGGCATAACGAGCTAGGCGATTAAAGTCATGGAGGTACTCTATGACAGAACGGGATCCCTGATTGAGTGCGCTGAACTCT

Reverse complement sequence

AGAGTTCAGCGCACTCAATCAGGGATCCCGTTCTGTCATAGAGTACCTCCATGACTTTAATCGCCTAGCTCGTTATGCCCCAGAGGATGTTCGCACTGAT[AGAGAACG/AGAGAACA,G]
TCAGGAGAAGTTTTTAGAGGGACTGAATGATGAGTTGTCTTATGCATTACTGGCTATGGAATAACGGGATTTCCAGCAGTTGGTGGACAAGGCGATTCGC

Allele Frequencies:

Populations	Population Size	Frequency of CGTTCTCT(primary allele)	Frequency of TGTTCTCT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	12.80%	13.54%	10.33%	C: 0.57%
All Indica	2759	40.40%	20.80%	21.75%	16.09%	C: 0.87%
All Japonica	1512	97.20%	0.30%	0.73%	1.79%	NA
Aus	269	82.90%	6.70%	7.43%	1.86%	C: 1.12%
Indica I	595	62.40%	17.50%	15.46%	4.71%	NA
Indica II	465	38.50%	24.30%	19.14%	17.85%	C: 0.22%
Indica III	913	25.60%	18.90%	26.94%	26.07%	C: 2.41%
Indica Intermediate	786	42.20%	23.50%	22.01%	12.09%	C: 0.13%
Temperate Japonica	767	99.30%	0.10%	0.52%	0.00%	NA
Tropical Japonica	504	93.50%	0.80%	0.99%	4.76%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	68.90%	10.00%	8.89%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112969673	CGTTCTCT -> TGTTCTCT	LOC_Os11g22550.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:10.913; most accessible tissue: Callus, score: 26.402	N	N	N	N
vg1112969673	CGTTCTCT -> DEL	LOC_Os11g22550.1	N	splice_donor_variant	Average:10.913; most accessible tissue: Callus, score: 26.402	N	N	N	N
vg1112969673	CGTTCTCT -> C	LOC_Os11g22550.1	frameshift_variant&splice_region_variant ; p.Arg183fs; HIGH	frameshift_variant	Average:10.913; most accessible tissue: Callus, score: 26.402	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112969673	6.91E-07	9.38E-07	mr1654	Ind_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