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Detailed information for vg0819479739:

Variant ID: vg0819479739 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19479739
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTCTCTCGGTTCATTTGTGATGCTAACTGATACTAAGTTGTGATGTAATTCAAATTATTGTTGATAACCGATAATTTGGTAAATTATTGATTTTATTT[C/T]
TCTTTATTAAATTACATATCTTTCAAGTTATTATTCAAGTGAGATCCATTGGGTACCCGCCGGATATACCCGCGCCCGCTGGGCATGGGCACGGGCACGG

Reverse complement sequence

CCGTGCCCGTGCCCATGCCCAGCGGGCGCGGGTATATCCGGCGGGTACCCAATGGATCTCACTTGAATAATAACTTGAAAGATATGTAATTTAATAAAGA[G/A]
AAATAAAATCAATAATTTACCAAATTATCGGTTATCAACAATAATTTGAATTACATCACAACTTAGTATCAGTTAGCATCACAAATGAACCGAGAGAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.70%	4.80%	1.46%	0.00%	NA
All Indica	2759	98.30%	0.30%	1.49%	0.00%	NA
All Japonica	1512	84.10%	14.40%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	0.30%	1.51%	0.00%	NA
Indica II	465	99.10%	0.00%	0.86%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	96.20%	0.50%	3.31%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	57.10%	38.50%	4.37%	0.00%	NA
Japonica Intermediate	241	90.00%	9.50%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	5.60%	5.56%	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
vg0819479739	C -> T	LOC_Os08g31480-LOC_Os08g31510	intergenic_region ; MODIFIER	silent_mutation	Average:62.14; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819479739	2.41E-07	5.18E-10	mr1073	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
vg0819479739	7.01E-06	7.01E-06	mr1153	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
vg0819479739	NA	5.69E-06	mr1262	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
vg0819479739	8.82E-06	8.82E-06	mr1266	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
vg0819479739	NA	2.01E-06	mr1345	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
vg0819479739	NA	5.44E-06	mr1388	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
vg0819479739	2.34E-06	2.34E-06	mr1601	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
vg0819479739	NA	1.71E-07	mr1606	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
vg0819479739	3.69E-06	8.46E-07	mr1819	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
vg0819479739	NA	2.18E-08	mr1830	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
vg0819479739	5.26E-06	1.69E-10	mr1852	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
vg0819479739	NA	3.81E-07	mr1866	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