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Detailed information for vg0335572253:

Variant ID: vg0335572253 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35572253
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTGCTCCCCCGCTACCCCGGGCTCGAGAGTCTCGCACTTGTGCTAACACATGACTACCCGAGATGCGTCCATATCTGGTCGGGGAAGGATGGCTCGGA[C/T]
GACGACGCGACGGGCGGAGTAGGCCGGCCGTGCTCACCCACCGCCGCCACGCTCTTCGTCTAGCCACCTCCGCCGGTGCGGCCCCCTTCTCCGCCCACCA

Reverse complement sequence

TGGTGGGCGGAGAAGGGGGCCGCACCGGCGGAGGTGGCTAGACGAAGAGCGTGGCGGCGGTGGGTGAGCACGGCCGGCCTACTCCGCCCGTCGCGTCGTC[G/A]
TCCGAGCCATCCTTCCCCGACCAGATATGGACGCATCTCGGGTAGTCATGTGTTAGCACAAGTGCGAGACTCTCGAGCCCGGGGTAGCGGGGGAGCACGG

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	67.90%	30.60%	1.02%	0.44%	NA
All Indica	2759	74.40%	23.20%	1.59%	0.76%	NA
All Japonica	1512	54.50%	45.40%	0.13%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	60.20%	34.80%	5.04%	0.00%	NA
Indica II	465	49.00%	51.00%	0.00%	0.00%	NA
Indica III	913	92.90%	4.60%	0.22%	2.30%	NA
Indica Intermediate	786	78.90%	19.60%	1.53%	0.00%	NA
Temperate Japonica	767	89.40%	10.40%	0.13%	0.00%	NA
Tropical Japonica	504	10.30%	89.70%	0.00%	0.00%	NA
Japonica Intermediate	241	35.70%	63.90%	0.41%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	60.00%	37.80%	2.22%	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
vg0335572253	C -> T	LOC_Os03g62880.1	intron_variant ; MODIFIER	silent_mutation	Average:76.538; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0335572253	C -> DEL	N	N	silent_mutation	Average:76.538; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335572253	NA	4.66E-06	mr1091	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
vg0335572253	NA	6.49E-06	mr1227	Ind_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
vg0335572253	NA	2.84E-06	mr1229	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
vg0335572253	NA	3.51E-07	mr1536	Ind_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
vg0335572253	NA	9.43E-06	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
vg0335572253	1.28E-06	1.27E-06	mr1873	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
vg0335572253	NA	3.01E-07	mr1229_2	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
vg0335572253	NA	2.35E-06	mr1383_2	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