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Detailed information for vg0807724740:

Variant ID: vg0807724740 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7724740
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCTCGTGAAGTCCGTTGCGAAGATCTCTCTCACACGATGTCCATACACCGTATGGCATTTTGTATCCAACTTCGTCACCCGGTATCCTTGACTGTCTG[G/T]
ACCTCAGCTCCTCTCTGGGTCTAGTCCTGATCCCCACCATTGACCGAAGTTGACCTTTAAGAATTCTGACTCTAGTCACCTTCTCACATGGTATCCCGAC

Reverse complement sequence

GTCGGGATACCATGTGAGAAGGTGACTAGAGTCAGAATTCTTAAAGGTCAACTTCGGTCAATGGTGGGGATCAGGACTAGACCCAGAGAGGAGCTGAGGT[C/A]
CAGACAGTCAAGGATACCGGGTGACGAAGTTGGATACAAAATGCCATACGGTGTATGGACATCGTGTGAGAGAGATCTTCGCAACGGACTTCACGAGGTG

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	48.00%	4.50%	2.69%	44.73%	NA
All Indica	2759	27.70%	0.40%	4.35%	67.56%	NA
All Japonica	1512	84.60%	12.90%	0.40%	2.12%	NA
Aus	269	60.60%	0.00%	0.00%	39.41%	NA
Indica I	595	11.80%	0.00%	2.35%	85.88%	NA
Indica II	465	34.80%	1.70%	4.30%	59.14%	NA
Indica III	913	33.80%	0.00%	3.72%	62.43%	NA
Indica Intermediate	786	28.20%	0.50%	6.62%	64.63%	NA
Temperate Japonica	767	82.90%	15.40%	0.52%	1.17%	NA
Tropical Japonica	504	92.90%	3.80%	0.20%	3.17%	NA
Japonica Intermediate	241	72.60%	24.10%	0.41%	2.90%	NA
VI/Aromatic	96	19.80%	2.10%	1.04%	77.08%	NA
Intermediate	90	51.10%	6.70%	0.00%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807724740	G -> T	LOC_Os08g13010.1	intron_variant ; MODIFIER	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 75.058	N	N	N	N
vg0807724740	G -> DEL	N	N	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 75.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807724740	8.12E-06	8.12E-06	mr1008	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
vg0807724740	7.20E-06	7.20E-06	mr1009	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
vg0807724740	9.37E-07	NA	mr1588_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