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Detailed information for vg1001395945:

Variant ID: vg1001395945 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1395945
Reference Allele: G	Alternative Allele: T
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: 100. )

Flanking Sequence (100 bp) in Reference Genome:

ACACCTTCGCCTGAGATCTGCACCGGGTAGGCGGGTGATCAGGTTTGTGGGGAGTGCTTCTCGCACGACTGCTCGTCCTCGTCCACCATGTCTACGCCTG[G/T]
AGCCGGAGCTGCCGCCGGCGCCGCCGCCGCTGCTGCTGCTAGAGGAGATGGCGCGCCTGGAGCTGGAGCCGGAGATGGCACGCCTGGAGCCGGTGCCGCG

Reverse complement sequence

CGCGGCACCGGCTCCAGGCGTGCCATCTCCGGCTCCAGCTCCAGGCGCGCCATCTCCTCTAGCAGCAGCAGCGGCGGCGGCGCCGGCGGCAGCTCCGGCT[C/A]
CAGGCGTAGACATGGTGGACGAGGACGAGCAGTCGTGCGAGAAGCACTCCCCACAAACCTGATCACCCGCCTACCCGGTGCAGATCTCAGGCGAAGGTGT

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	84.70%	13.10%	1.14%	1.04%	NA
All Indica	2759	74.60%	22.20%	1.49%	1.67%	NA
All Japonica	1512	99.70%	0.20%	0.13%	0.00%	NA
Aus	269	97.40%	0.00%	2.60%	0.00%	NA
Indica I	595	61.20%	37.60%	0.50%	0.67%	NA
Indica II	465	72.30%	27.10%	0.43%	0.22%	NA
Indica III	913	81.60%	12.40%	3.18%	2.85%	NA
Indica Intermediate	786	78.10%	19.10%	0.89%	1.91%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	91.70%	1.00%	4.17%	3.12%	NA
Intermediate	90	95.60%	4.40%	0.00%	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
vg1001395945	G -> T	LOC_Os10g03300.1	missense_variant ; p.Gly5Val; MODERATE	nonsynonymous_codon ; G5V	Average:55.126; most accessible tissue: Zhenshan97 flag leaf, score: 79.481	unknown	unknown	DELETERIOUS	0.00
vg1001395945	G -> DEL	LOC_Os10g03300.1	N	frameshift_variant	Average:55.126; most accessible tissue: Zhenshan97 flag leaf, score: 79.481	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001395945	2.35E-09	NA	mr1486	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
vg1001395945	9.35E-10	3.56E-14	mr1486	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
vg1001395945	3.75E-07	NA	mr1548	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
vg1001395945	1.27E-07	4.88E-10	mr1548	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
vg1001395945	6.48E-09	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
vg1001395945	3.11E-08	4.94E-12	mr1721	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
vg1001395945	1.41E-07	NA	mr1486_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
vg1001395945	3.47E-08	1.95E-13	mr1486_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
vg1001395945	7.83E-12	NA	mr1721_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
vg1001395945	1.28E-11	1.49E-14	mr1721_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