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Detailed information for vg0810847739:

Variant ID: vg0810847739 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10847739
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GATTGCACGTTCCCATTGGACGCTCCGGGAAAACTCTTGAGGCCGCTACAACCATTGCTATCCCTGGGAGAACATATAATGAAGAGTTCATACCCGATGC[G/A]
TATGCCAAGGTGCAGCCGCAAGTGGTCCATGAAGGGTTTGAGTCCTACGACATTGACTTCCCGACTGCAGATGGTGTATCCGTACTTGGGGATGCGGTCG

Reverse complement sequence

CGACCGCATCCCCAAGTACGGATACACCATCTGCAGTCGGGAAGTCAATGTCGTAGGACTCAAACCCTTCATGGACCACTTGCGGCTGCACCTTGGCATA[C/T]
GCATCGGGTATGAACTCTTCATTATATGTTCTCCCAGGGATAGCAATGGTTGTAGCGGCCTCAAGAGTTTTCCCGGAGCGTCCAATGGGAACGTGCAATC

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	82.60%	16.10%	0.91%	0.32%	NA
All Indica	2759	97.80%	1.40%	0.69%	0.14%	NA
All Japonica	1512	65.10%	34.80%	0.13%	0.00%	NA
Aus	269	52.40%	35.30%	8.18%	4.09%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	98.90%	0.80%	0.33%	0.00%	NA
Indica Intermediate	786	94.30%	3.40%	1.78%	0.51%	NA
Temperate Japonica	767	94.80%	5.20%	0.00%	0.00%	NA
Tropical Japonica	504	31.90%	67.70%	0.40%	0.00%	NA
Japonica Intermediate	241	39.80%	60.20%	0.00%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	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
vg0810847739	G -> A	LOC_Os08g17740.1	synonymous_variant ; p.Ala101Ala; LOW	synonymous_codon	Average:43.014; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0810847739	G -> DEL	LOC_Os08g17740.1	N	frameshift_variant	Average:43.014; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810847739	NA	3.80E-07	mr1229	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
vg0810847739	NA	1.47E-06	mr1330	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
vg0810847739	NA	1.95E-08	mr1449	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
vg0810847739	4.16E-06	NA	mr1136_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
vg0810847739	NA	1.77E-09	mr1449_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
vg0810847739	NA	5.12E-14	mr1552_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
vg0810847739	NA	3.87E-09	mr1642_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
vg0810847739	NA	4.04E-08	mr1696_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