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Detailed information for vg0503172777:

Variant ID: vg0503172777 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3172777
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAAGGTCAGTGATATGAGAAAATATCTCAATCGGGCATCCGGCCATCACGGATGACACACATCTCAATCGGGCCAACACAAAAGCCCATCACGGATGA[T/C]
TGTCATCTCTAACGGGTCTAAACTATAGCCCATCACGGATGGCTCTCATCTCTAACGGGCCTAAAATATAGCCCATCACGGATGACTCTCATCTCTAACA

Reverse complement sequence

TGTTAGAGATGAGAGTCATCCGTGATGGGCTATATTTTAGGCCCGTTAGAGATGAGAGCCATCCGTGATGGGCTATAGTTTAGACCCGTTAGAGATGACA[A/G]
TCATCCGTGATGGGCTTTTGTGTTGGCCCGATTGAGATGTGTGTCATCCGTGATGGCCGGATGCCCGATTGAGATATTTTCTCATATCACTGACCTTTGC

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	76.40%	11.10%	10.50%	1.99%	NA
All Indica	2759	98.40%	0.50%	0.91%	0.14%	NA
All Japonica	1512	34.80%	32.70%	28.04%	4.43%	NA
Aus	269	95.50%	1.10%	3.35%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.30%	0.20%	1.29%	0.22%	NA
Indica III	913	97.80%	1.00%	0.99%	0.22%	NA
Indica Intermediate	786	98.20%	0.50%	1.15%	0.13%	NA
Temperate Japonica	767	33.60%	32.90%	29.20%	4.30%	NA
Tropical Japonica	504	34.10%	30.40%	30.36%	5.16%	NA
Japonica Intermediate	241	39.80%	37.30%	19.50%	3.32%	NA
VI/Aromatic	96	55.20%	2.10%	20.83%	21.88%	NA
Intermediate	90	67.80%	10.00%	20.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0503172777	T -> DEL	N	N	silent_mutation	Average:41.999; most accessible tissue: Callus, score: 57.485	N	N	N	N
vg0503172777	T -> C	LOC_Os05g06240-LOC_Os05g06250	intergenic_region ; MODIFIER	silent_mutation	Average:41.999; most accessible tissue: Callus, score: 57.485	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503172777	NA	5.90E-06	mr1397	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
vg0503172777	1.12E-07	NA	mr1768	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
vg0503172777	NA	2.23E-06	mr1768	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