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Detailed information for vg0118595835:

Variant ID: vg0118595835 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18595835
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.19, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTCTGCCCGTGCCCGACCCAGCCCGCTGCCATCCCTAATAAAATTCGATGATCCACAATCTTGCTATTGATCATCATATCAGACTTGGGATTTATAA[T/C]
GTAGTTGCTCCTGACTGATAATGTCGTAAGCTGAATGTCACAATATCCACTCTGAGAATCTGTTTCTGCAGTTATATTAGTTCCTTAAAGAACTTTGACA

Reverse complement sequence

TGTCAAAGTTCTTTAAGGAACTAATATAACTGCAGAAACAGATTCTCAGAGTGGATATTGTGACATTCAGCTTACGACATTATCAGTCAGGAGCAACTAC[A/G]
TTATAAATCCCAAGTCTGATATGATGATCAATAGCAAGATTGTGGATCATCGAATTTTATTAGGGATGGCAGCGGGCTGGGTCGGGCACGGGCAGAGTGA

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	61.40%	38.50%	0.08%	0.00%	NA
All Indica	2759	92.50%	7.40%	0.07%	0.00%	NA
All Japonica	1512	10.60%	89.30%	0.07%	0.00%	NA
Aus	269	55.40%	44.60%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	84.50%	15.10%	0.43%	0.00%	NA
Indica III	913	93.20%	6.80%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.80%	0.00%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	17.30%	82.70%	0.00%	0.00%	NA
Japonica Intermediate	241	26.60%	73.00%	0.41%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	1.11%	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
vg0118595835	T -> C	LOC_Os01g33784.1	intron_variant ; MODIFIER	silent_mutation	Average:71.492; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118595835	1.78E-06	1.78E-06	mr1065	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
vg0118595835	NA	3.08E-06	mr1428	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
vg0118595835	NA	6.14E-09	mr1946_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
vg0118595835	NA	6.14E-09	mr1948_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