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Detailed information for vg0317333132:

Variant ID: vg0317333132 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17333132
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGATGGTGTAGCCAAATAATATTGCCATGCCAACTAGACTAGCATGACCAAATAACGTTGCCACGCTAATCAGACCGGTATGGTAGTATGGTTTTGCCG[T/C]
GTCAGTCTGTTAGCGTGGTTATAAGGTTATATCTTGAAAATAAGTTTTGGAAGGTTTATTTTTAAAAGTAAAGTTTAAAAAGTTTATAAAAAAAGTGATA

Reverse complement sequence

TATCACTTTTTTTATAAACTTTTTAAACTTTACTTTTAAAAATAAACCTTCCAAAACTTATTTTCAAGATATAACCTTATAACCACGCTAACAGACTGAC[A/G]
CGGCAAAACCATACTACCATACCGGTCTGATTAGCGTGGCAACGTTATTTGGTCATGCTAGTCTAGTTGGCATGGCAATATTATTTGGCTACACCATCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	8.30%	0.72%	0.00%	NA
All Indica	2759	99.20%	0.70%	0.11%	0.00%	NA
All Japonica	1512	73.70%	24.50%	1.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.30%	0.25%	0.00%	NA
Temperate Japonica	767	92.70%	5.60%	1.69%	0.00%	NA
Tropical Japonica	504	49.80%	49.00%	1.19%	0.00%	NA
Japonica Intermediate	241	63.10%	33.60%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	4.44%	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
vg0317333132	T -> C	LOC_Os03g30400.1	downstream_gene_variant ; 2462.0bp to feature; MODIFIER	silent_mutation	Average:79.129; most accessible tissue: Minghui63 root, score: 85.467	N	N	N	N
vg0317333132	T -> C	LOC_Os03g30390-LOC_Os03g30400	intergenic_region ; MODIFIER	silent_mutation	Average:79.129; most accessible tissue: Minghui63 root, score: 85.467	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317333132	2.58E-07	NA	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317333132	6.61E-06	NA	Grain_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317333132	NA	5.43E-10	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0317333132	1.42E-06	NA	mr1082	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
vg0317333132	6.10E-07	NA	mr1104	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
vg0317333132	NA	3.14E-07	mr1104	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
vg0317333132	6.88E-07	NA	mr1408	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
vg0317333132	NA	8.37E-06	mr1620	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
vg0317333132	NA	3.47E-06	mr1873_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