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Detailed information for vg0221812870:

Variant ID: vg0221812870 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21812870
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGCGTCCAGGAACTCGTCGCGGTGGCTGCACCGGCCGCCGACGGAGCTCACCATCACGATGTCGTTGGCGAGCTTGCTGATCCTCTCGTTGAGGTTCAC[G/A]
CCAGCGTCGCCGCCCGCGCCCGCGTCGGCGGCCAGCTCACGCACGAGCCGCGCCACCTCGCGCTCTCGGACGCCCTGGAACGACCTCACCCGGGCGGCGG

Reverse complement sequence

CCGCCGCCCGGGTGAGGTCGTTCCAGGGCGTCCGAGAGCGCGAGGTGGCGCGGCTCGTGCGTGAGCTGGCCGCCGACGCGGGCGCGGGCGGCGACGCTGG[C/T]
GTGAACCTCAACGAGAGGATCAGCAAGCTCGCCAACGACATCGTGATGGTGAGCTCCGTCGGCGGCCGGTGCAGCCACCGCGACGAGTTCCTGGACGCGC

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	94.10%	5.70%	0.25%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	81.90%	17.40%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	92.80%	6.10%	1.04%	0.00%	NA
Tropical Japonica	504	69.20%	30.60%	0.20%	0.00%	NA
Japonica Intermediate	241	73.40%	25.70%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0221812870	G -> A	LOC_Os02g36190.1	synonymous_variant ; p.Gly174Gly; LOW	synonymous_codon	Average:56.009; most accessible tissue: Zhenshan97 flag leaf, score: 85.388	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221812870	NA	5.72E-07	mr1502	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
vg0221812870	NA	4.20E-06	mr1502	Jap_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
vg0221812870	1.07E-09	1.38E-11	mr1543	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
vg0221812870	6.33E-07	4.51E-11	mr1543	Jap_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
vg0221812870	3.52E-06	NA	mr1745	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
vg0221812870	1.30E-22	5.28E-35	mr1871	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
vg0221812870	4.87E-09	4.91E-17	mr1871	Jap_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
vg0221812870	1.32E-24	6.32E-43	mr1042_2	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
vg0221812870	5.16E-14	2.49E-19	mr1042_2	Jap_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
vg0221812870	8.07E-08	3.05E-12	mr1502_2	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
vg0221812870	NA	5.55E-09	mr1502_2	Jap_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
vg0221812870	4.81E-14	1.06E-17	mr1543_2	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
vg0221812870	1.90E-09	4.96E-14	mr1543_2	Jap_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
vg0221812870	5.83E-12	2.94E-19	mr1680_2	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
vg0221812870	1.06E-07	1.55E-10	mr1680_2	Jap_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
vg0221812870	8.73E-16	1.04E-25	mr1742_2	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
vg0221812870	8.51E-10	4.86E-15	mr1742_2	Jap_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
vg0221812870	3.34E-09	NA	mr1745_2	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
vg0221812870	2.99E-45	4.72E-67	mr1871_2	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
vg0221812870	1.49E-20	1.49E-30	mr1871_2	Jap_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