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Detailed information for vg1012383116:

Variant ID: vg1012383116 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12383116
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACTGAAGACTCTCCTATATCAAAAGTGATGGGAGAGTTAGGGAATCGGGACTTACCCTTGACCAGGAATCGATCCTGAGCCGCGAGGGCTTTGGATTC[G/T,A]
TCTCCCTGGTGATTCTCGGTTTCGCCGTGCCCGATGGGCGTTGGGGTCGTCATCCCCGATGCCGCTGCAGGTGAGTTCTCCAGAACCGTCACCCTTGCGG

Reverse complement sequence

CCGCAAGGGTGACGGTTCTGGAGAACTCACCTGCAGCGGCATCGGGGATGACGACCCCAACGCCCATCGGGCACGGCGAAACCGAGAATCACCAGGGAGA[C/A,T]
GAATCCAAAGCCCTCGCGGCTCAGGATCGATTCCTGGTCAAGGGTAAGTCCCGATTCCCTAACTCTCCCATCACTTTTGATATAGGAGAGTCTTCAGTTC

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	80.90%	3.90%	2.20%	9.27%	T: 3.83%
All Indica	2759	75.70%	6.50%	3.15%	8.16%	T: 6.49%
All Japonica	1512	90.50%	0.00%	0.66%	8.86%	NA
Aus	269	97.00%	0.00%	0.74%	2.23%	NA
Indica I	595	87.70%	0.00%	3.70%	8.07%	T: 0.50%
Indica II	465	83.00%	3.20%	3.44%	3.87%	T: 6.45%
Indica III	913	65.60%	14.60%	1.86%	10.30%	T: 7.67%
Indica Intermediate	786	74.00%	3.90%	4.07%	8.27%	T: 9.67%
Temperate Japonica	767	98.00%	0.00%	0.26%	1.69%	NA
Tropical Japonica	504	82.30%	0.00%	0.99%	16.67%	NA
Japonica Intermediate	241	83.40%	0.00%	1.24%	15.35%	NA
VI/Aromatic	96	34.40%	1.00%	3.12%	61.46%	NA
Intermediate	90	77.80%	2.20%	2.22%	15.56%	T: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012383116	G -> T	LOC_Os10g24170.1	missense_variant ; p.Asp97Glu; MODERATE	nonsynonymous_codon ; D97E	Average:52.349; most accessible tissue: Zhenshan97 panicle, score: 67.02	unknown	unknown	TOLERATED	0.91
vg1012383116	G -> A	LOC_Os10g24170.1	synonymous_variant ; p.Asp97Asp; LOW	synonymous_codon	Average:52.349; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1012383116	G -> DEL	LOC_Os10g24170.1	N	frameshift_variant	Average:52.349; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012383116	2.40E-06	2.40E-06	mr1770	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