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Detailed information for vg1004377181:

Variant ID: vg1004377181 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4377181
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGCGCAACTTGAATGCAATGCCGAGCTAGATATGGAACACAAGAAGCTAGCCGATCTCCCAAAATCAATTGAAGAACAAAAATCAAGGCTCAAATC[A/G]
GCTATCAAGAATGTTGCCGACCTAACCAAGTCCCTGAAAGTCATCTCTGGAACTGATGCTCAACATGCCCAAGCTATTGAAGAAAAAGAACAAATTAGGC

Reverse complement sequence

GCCTAATTTGTTCTTTTTCTTCAATAGCTTGGGCATGTTGAGCATCAGTTCCAGAGATGACTTTCAGGGACTTGGTTAGGTCGGCAACATTCTTGATAGC[T/C]
GATTTGAGCCTTGATTTTTGTTCTTCAATTGATTTTGGGAGATCGGCTAGCTTCTTGTGTTCCATATCTAGCTCGGCATTGCATTCAAGTTGCGCCAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.30%	16.00%	2.29%	40.41%	NA
All Indica	2759	31.20%	16.30%	3.84%	48.64%	NA
All Japonica	1512	67.70%	1.10%	0.07%	31.15%	NA
Aus	269	1.50%	93.30%	0.00%	5.20%	NA
Indica I	595	35.80%	42.40%	1.85%	20.00%	NA
Indica II	465	38.10%	10.50%	1.51%	49.89%	NA
Indica III	913	22.10%	3.30%	6.24%	68.35%	NA
Indica Intermediate	786	34.10%	15.30%	3.94%	46.69%	NA
Temperate Japonica	767	89.40%	0.30%	0.00%	10.30%	NA
Tropical Japonica	504	32.70%	2.00%	0.20%	65.08%	NA
Japonica Intermediate	241	71.40%	2.10%	0.00%	26.56%	NA
VI/Aromatic	96	31.20%	19.80%	0.00%	48.96%	NA
Intermediate	90	37.80%	21.10%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004377181	A -> G	LOC_Os10g08080.1	synonymous_variant ; p.Ser845Ser; LOW	synonymous_codon	Average:22.483; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg1004377181	A -> DEL	LOC_Os10g08080.1	N	frameshift_variant	Average:22.483; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004377181	NA	2.47E-07	mr1090	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
vg1004377181	6.59E-06	2.38E-07	mr1094	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
vg1004377181	NA	1.72E-06	mr1096	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
vg1004377181	NA	2.24E-06	mr1068_2	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
vg1004377181	8.86E-07	2.04E-09	mr1090_2	Jap_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