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Detailed information for vg1011368532:

Variant ID: vg1011368532 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11368532
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGACGAGTCTTGATTCCCCCACTCAGCGGTAGCCCCTTTTCTCCTCCCGCCCTGTTTGCCGCACCTTGCTGCGGGTACGGTGTGGTGAAAGGCAAAATC[G/A]
CAGCTTGTGCGTGAGGTTGGGCCGTGGCATTCGACTGCCCGGTTCCAACTGGAGGTACTTGCTGAGCCACCATAGATGGGTCAAAAATTGGCTGCGACCA

Reverse complement sequence

TGGTCGCAGCCAATTTTTGACCCATCTATGGTGGCTCAGCAAGTACCTCCAGTTGGAACCGGGCAGTCGAATGCCACGGCCCAACCTCACGCACAAGCTG[C/T]
GATTTTGCCTTTCACCACACCGTACCCGCAGCAAGGTGCGGCAAACAGGGCGGGAGGAGAAAAGGGGCTACCGCTGAGTGGGGGAATCAAGACTCGTCCA

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	56.50%	1.30%	5.14%	37.09%	NA
All Indica	2759	53.90%	2.20%	5.47%	38.42%	NA
All Japonica	1512	61.80%	0.00%	2.45%	35.78%	NA
Aus	269	48.00%	0.40%	15.99%	35.69%	NA
Indica I	595	35.00%	1.00%	3.87%	60.17%	NA
Indica II	465	64.70%	1.50%	4.09%	29.68%	NA
Indica III	913	61.40%	3.80%	6.57%	28.15%	NA
Indica Intermediate	786	53.20%	1.50%	6.23%	39.06%	NA
Temperate Japonica	767	72.50%	0.00%	0.91%	26.60%	NA
Tropical Japonica	504	54.60%	0.00%	4.76%	40.67%	NA
Japonica Intermediate	241	42.70%	0.00%	2.49%	54.77%	NA
VI/Aromatic	96	64.60%	0.00%	6.25%	29.17%	NA
Intermediate	90	61.10%	1.10%	6.67%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011368532	G -> A	LOC_Os10g22010.1	missense_variant ; p.Ala472Val; MODERATE	nonsynonymous_codon ; A472V	Average:13.026; most accessible tissue: Callus, score: 28.846	benign	0.572	TOLERATED	0.60
vg1011368532	G -> DEL	LOC_Os10g22010.1	N	frameshift_variant	Average:13.026; most accessible tissue: Callus, score: 28.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011368532	7.31E-06	1.49E-07	mr1080	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
vg1011368532	NA	3.54E-06	mr1140	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
vg1011368532	NA	4.78E-06	mr1203	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
vg1011368532	4.38E-08	2.68E-10	mr1238	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
vg1011368532	9.66E-07	4.91E-09	mr1309	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
vg1011368532	NA	4.08E-07	mr1613	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
vg1011368532	NA	8.67E-06	mr1618	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
vg1011368532	9.01E-06	1.37E-06	mr1795	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
vg1011368532	NA	1.39E-07	mr1841	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
vg1011368532	2.28E-06	2.28E-06	mr1900	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
vg1011368532	NA	7.98E-07	mr1238_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
vg1011368532	NA	7.70E-07	mr1484_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
vg1011368532	NA	3.49E-09	mr1841_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
vg1011368532	NA	1.27E-08	mr1900_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