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Detailed information for vg0402677786:

Variant ID: vg0402677786 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2677786
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGACTTGTTGCACCACCAATTCCGAATCACCAAAGGCCTCCACATATTTAGATCCAACCATCTCCATAACTTGTAAGCCGAACAATAAAGCATTGTATTC[G/A]
GCTTGATTATTTGTGCAATAATATTCCAAACGAACCGATGCCTCATAACACATGCCATTAGGTGAAAACAAAACTACCCCTATGCCTTGACCTTCTTTGC

Reverse complement sequence

GCAAAGAAGGTCAAGGCATAGGGGTAGTTTTGTTTTCACCTAATGGCATGTGTTATGAGGCATCGGTTCGTTTGGAATATTATTGCACAAATAATCAAGC[C/T]
GAATACAATGCTTTATTGTTCGGCTTACAAGTTATGGAGATGGTTGGATCTAAATATGTGGAGGCCTTTGGTGATTCGGAATTGGTGGTGCAACAAGTCG

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	92.00%	1.50%	0.13%	6.35%	NA
All Indica	2759	99.60%	0.20%	0.04%	0.14%	NA
All Japonica	1512	76.40%	3.70%	0.33%	19.58%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.00%	0.25%	NA
Temperate Japonica	767	90.00%	4.40%	0.00%	5.61%	NA
Tropical Japonica	504	58.50%	3.80%	0.79%	36.90%	NA
Japonica Intermediate	241	70.50%	1.20%	0.41%	27.80%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	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
vg0402677786	G -> DEL	N	N	silent_mutation	Average:9.265; most accessible tissue: Callus, score: 31.537	N	N	N	N
vg0402677786	G -> A	LOC_Os04g05370.1	intron_variant ; MODIFIER	silent_mutation	Average:9.265; most accessible tissue: Callus, score: 31.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402677786	1.63E-08	1.63E-08	mr1068	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
vg0402677786	1.22E-06	6.19E-07	mr1211	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