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Detailed information for vg0316684121:

Variant ID: vg0316684121 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16684121
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CTTACATTCCTGGGATCCTTAGAAAATTATGGGTGTTTTGCATCAAATGTCTTCCACTGGCGAGCATCGGCGAGATGTCGAATCATACCATCTATCTTCC[A/G]
GCTCTCTTGATGCCATCTCATCAACTCAGCATCAGTCGGGTTTGAGTACAGGCGCTTCAGGCGGTCCTTAATTGGTAGGTACCACATCACCATTGAGGGA

Reverse complement sequence

TCCCTCAATGGTGATGTGGTACCTACCAATTAAGGACCGCCTGAAGCGCCTGTACTCAAACCCGACTGATGCTGAGTTGATGAGATGGCATCAAGAGAGC[T/C]
GGAAGATAGATGGTATGATTCGACATCTCGCCGATGCTCGCCAGTGGAAGACATTTGATGCAAAACACCCATAATTTTCTAAGGATCCCAGGAATGTAAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	32.80%	8.08%	1.10%	NA
All Indica	2759	41.00%	46.40%	11.42%	1.27%	NA
All Japonica	1512	90.90%	4.20%	4.03%	0.79%	NA
Aus	269	29.40%	70.60%	0.00%	0.00%	NA
Indica I	595	12.90%	67.70%	18.32%	1.01%	NA
Indica II	465	84.10%	13.10%	2.58%	0.22%	NA
Indica III	913	37.30%	49.80%	10.84%	1.97%	NA
Indica Intermediate	786	40.80%	45.80%	12.09%	1.27%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	74.80%	12.10%	11.51%	1.59%	NA
Japonica Intermediate	241	96.70%	0.80%	0.83%	1.66%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	73.30%	20.00%	4.44%	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
vg0316684121	A -> DEL	LOC_Os03g29310.1	N	frameshift_variant	Average:36.864; most accessible tissue: Minghui63 flag leaf, score: 50.629	N	N	N	N
vg0316684121	A -> G	LOC_Os03g29310.1	missense_variant ; p.Trp186Arg; MODERATE	nonsynonymous_codon ; W186R	Average:36.864; most accessible tissue: Minghui63 flag leaf, score: 50.629	benign	-0.417	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316684121	1.82E-14	7.04E-18	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
vg0316684121	2.12E-15	2.78E-52	Grain_length	Ind_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
vg0316684121	NA	9.53E-16	Grain_width	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
vg0316684121	NA	1.61E-06	mr1502	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
vg0316684121	NA	9.92E-07	mr1542	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
vg0316684121	NA	5.24E-10	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
vg0316684121	NA	7.70E-07	mr1720	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
vg0316684121	NA	9.36E-07	mr1727	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
vg0316684121	NA	4.57E-07	mr1942	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
vg0316684121	NA	2.76E-07	mr1482_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
vg0316684121	NA	3.27E-06	mr1542_2	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
vg0316684121	NA	5.78E-06	mr1567_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
vg0316684121	NA	9.33E-06	mr1739_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
vg0316684121	NA	2.86E-07	mr1931_2	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