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Detailed information for vg1000942377:

Variant ID: vg1000942377 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 942377
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TGACCGTTGGATCGTACCAAGACTTGCAGTTAGGTTTGGGTTTTTGACCCGTTTTTGTTCCGAGTATGTTTTGGCCTGCCCCCCTCCTCCACTCACGTCA[G/T,A]
CAGCTGAACTCGTCCCCGTTCTCACACGCGTCGCTGACTCGCTGCCATCATCTTCAGTTTAAATCTGTACATAGTGTATATGTAGATTCAAATTTAGGAT

Reverse complement sequence

ATCCTAAATTTGAATCTACATATACACTATGTACAGATTTAAACTGAAGATGATGGCAGCGAGTCAGCGACGCGTGTGAGAACGGGGACGAGTTCAGCTG[C/A,T]
TGACGTGAGTGGAGGAGGGGGGCAGGCCAAAACATACTCGGAACAAAAACGGGTCAAAAACCCAAACCTAACTGCAAGTCTTGGTACGATCCAACGGTCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.30%	1.40%	5.42%	13.80%	A: 0.04%
All Indica	2759	67.50%	2.00%	8.48%	22.04%	NA
All Japonica	1512	96.80%	0.00%	0.73%	2.45%	NA
Aus	269	92.90%	3.30%	3.35%	0.37%	NA
Indica I	595	60.30%	2.40%	11.93%	25.38%	NA
Indica II	465	62.80%	2.80%	8.60%	25.81%	NA
Indica III	913	71.70%	1.20%	6.90%	20.15%	NA
Indica Intermediate	786	70.60%	2.30%	7.63%	19.47%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	93.50%	0.00%	1.39%	5.16%	NA
Japonica Intermediate	241	95.40%	0.00%	0.83%	3.73%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	1.10%	2.22%	6.67%	A: 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
vg1000942377	G -> T	LOC_Os10g02509.1	upstream_gene_variant ; 1976.0bp to feature; MODIFIER	silent_mutation	Average:68.462; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1000942377	G -> T	LOC_Os10g02509-LOC_Os10g02520	intergenic_region ; MODIFIER	silent_mutation	Average:68.462; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1000942377	G -> A	LOC_Os10g02509.1	upstream_gene_variant ; 1976.0bp to feature; MODIFIER	silent_mutation	Average:68.462; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1000942377	G -> A	LOC_Os10g02509-LOC_Os10g02520	intergenic_region ; MODIFIER	silent_mutation	Average:68.462; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1000942377	G -> DEL	N	N	silent_mutation	Average:68.462; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000942377	1.08E-06	NA	mr1721	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