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Detailed information for vg0224323881:

Variant ID: vg0224323881 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24323881
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATTGCTCAACTGTCCACGAGTTCAGCATCGATCTGCAATCACTGCTAGATTTCAAGAAAGGCATCACGGAAAGATCCAAGCGGAGCCTTAAGTTCTTG[G/A]
AACACTAGCACTCACTTCTGTTGGTGGAAAGGTGTCATGTGCACCACTGCACGGCCGTTTCGCGTCTCAACGCTGAATCTCTCCGCCCAAAGCTTGGCAG

Reverse complement sequence

CTGCCAAGCTTTGGGCGGAGAGATTCAGCGTTGAGACGCGAAACGGCCGTGCAGTGGTGCACATGACACCTTTCCACCAACAGAAGTGAGTGCTAGTGTT[C/T]
CAAGAACTTAAGGCTCCGCTTGGATCTTTCCGTGATGCCTTTCTTGAAATCTAGCAGTGATTGCAGATCGATGCTGAACTCGTGGACAGTTGAGCAATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.30%	5.10%	4.87%	31.80%	NA
All Indica	2759	62.30%	3.20%	2.79%	31.75%	NA
All Japonica	1512	50.30%	7.50%	8.53%	33.66%	NA
Aus	269	64.70%	2.60%	5.95%	26.77%	NA
Indica I	595	74.10%	0.50%	0.67%	24.71%	NA
Indica II	465	60.90%	4.10%	1.51%	33.55%	NA
Indica III	913	58.30%	3.10%	4.05%	34.61%	NA
Indica Intermediate	786	58.90%	4.70%	3.69%	32.70%	NA
Temperate Japonica	767	38.90%	12.40%	3.26%	45.50%	NA
Tropical Japonica	504	72.40%	0.00%	14.68%	12.90%	NA
Japonica Intermediate	241	40.20%	7.90%	12.45%	39.42%	NA
VI/Aromatic	96	41.70%	29.20%	3.12%	26.04%	NA
Intermediate	90	67.80%	3.30%	5.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224323881	G -> A	LOC_Os02g40190.1	stop_gained ; p.Trp102*; HIGH	stop_gained	Average:45.1; most accessible tissue: Callus, score: 62.86	N	N	N	N
vg0224323881	G -> DEL	LOC_Os02g40190.1	N	frameshift_variant	Average:45.1; most accessible tissue: Callus, score: 62.86	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224323881	NA	1.39E-06	mr1952	Ind_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
vg0224323881	1.73E-08	NA	mr1113_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
vg0224323881	6.79E-06	NA	mr1120_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
vg0224323881	1.43E-06	5.40E-07	mr1123_2	Ind_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
vg0224323881	2.71E-06	NA	mr1150_2	Ind_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
vg0224323881	NA	9.60E-06	mr1247_2	Ind_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
vg0224323881	NA	2.27E-08	mr1567_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
vg0224323881	3.80E-06	2.65E-07	mr1748_2	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
vg0224323881	4.38E-07	5.69E-06	mr1961_2	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