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Detailed information for vg0317005591:

Variant ID: vg0317005591 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 17005591
Reference Allele: T	Alternative Allele: C,TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.37, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AAGACTTGTTACCTGGTCTCTCCACCATGTGACCCGGGTTCCACCTTTTAAGTCGTCACATCAACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTC[T/C,TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC]
ACCATGTGACCCATGGAAATTGTTCCGGGTTCCAAACCTTGGGCTCTGATACCCACTTGTTAGAGTGCGCAGCCCGGCCCACCAACCGTGGGCCACAACT

Reverse complement sequence

AGTTGTGGCCCACGGTTGGTGGGCCGGGCTGCGCACTCTAACAAGTGGGTATCAGAGCCCAAGGTTTGGAACCCGGAACAATTTCCATGGGTCACATGGT[A/G,GGAGAGGCCAGGTAACAAGTCTCCGGGGTCACATAGGTGGGTCACA]
GAGAGGCCAGGTAACAAGTCTCCGGGGTCACATAGGTTGATGTGACGACTTAAAAGGTGGAACCCGGGTCACATGGTGGAGAGACCAGGTAACAAGTCTT

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	52.30%	42.20%	1.27%	4.23%	TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC: 0.02%
All Indica	2759	34.50%	56.20%	2.07%	7.21%	NA
All Japonica	1512	95.80%	4.20%	0.00%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	4.40%	60.00%	7.06%	28.57%	NA
Indica II	465	74.00%	25.60%	0.43%	0.00%	NA
Indica III	913	31.00%	67.90%	0.55%	0.55%	NA
Indica Intermediate	786	38.20%	57.80%	1.02%	3.05%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	88.50%	11.50%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	58.90%	35.60%	3.33%	1.11%	TGTGACCCACCTATGTGACCCCGGAGACTTGTTACCTGGCCTCTCC: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0317005591	T -> C	LOC_Os03g29830.1	downstream_gene_variant ; 3279.0bp to feature; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> C	LOC_Os03g29850.1	downstream_gene_variant ; 2364.0bp to feature; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> C	LOC_Os03g29830-LOC_Os03g29850	intergenic_region ; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> DEL	N	N	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC	LOC_Os03g29830.1	downstream_gene_variant ; 3280.0bp to feature; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC	LOC_Os03g29850.1	downstream_gene_variant ; 2363.0bp to feature; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0317005591	T -> TGTGACCCACCTATGTGACCCCGGAGACTT GTTACCTGGCCTCTCC	LOC_Os03g29830-LOC_Os03g29850	intergenic_region ; MODIFIER	silent_mutation	Average:72.245; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317005591	5.60E-09	NA	Grain_length	All	YES	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
vg0317005591	2.13E-07	2.48E-33	Grain_length	Ind_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
vg0317005591	NA	4.86E-12	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
vg0317005591	NA	6.19E-07	Grain_weight	Ind_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
vg0317005591	NA	6.25E-15	mr1059	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
vg0317005591	NA	4.73E-15	mr1143	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
vg0317005591	NA	9.03E-16	mr1167	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
vg0317005591	NA	7.73E-08	mr1245	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
vg0317005591	NA	2.54E-10	mr1307	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
vg0317005591	NA	2.66E-10	mr1399	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
vg0317005591	NA	7.66E-09	mr1439	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
vg0317005591	NA	5.85E-07	mr1516	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
vg0317005591	NA	6.64E-09	mr1607	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
vg0317005591	NA	4.34E-06	mr1665	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
vg0317005591	NA	9.40E-15	mr1675	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
vg0317005591	NA	1.39E-07	mr1677	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
vg0317005591	NA	1.56E-08	mr1942	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
vg0317005591	NA	1.85E-15	mr1969	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