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Detailed information for vg0811308449:

Variant ID: vg0811308449 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11308449
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CACAGAATGAGAGAAGAGAGCAGTTAGGGACCGGAGAGAAGTAGAAAACCAAGAGAGGAGAGAGGAGCAGAGATAGGTGTGTACGGTGTACCTGCGCATC[T/C]
GGAGCACCGGAGTTGCCGTTGATGATAGAGATCAACGGATCTACAAGAAGAAGATAGCAGAGACTGGGTTTGGGGAGTGATGTGACAAAGAGCTCACGAA

Reverse complement sequence

TTCGTGAGCTCTTTGTCACATCACTCCCCAAACCCAGTCTCTGCTATCTTCTTCTTGTAGATCCGTTGATCTCTATCATCAACGGCAACTCCGGTGCTCC[A/G]
GATGCGCAGGTACACCGTACACACCTATCTCTGCTCCTCTCTCCTCTCTTGGTTTTCTACTTCTCTCCGGTCCCTAACTGCTCTCTTCTCTCATTCTGTG

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	70.80%	29.20%	0.04%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	17.10%	82.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	5.30%	94.70%	0.00%	0.00%	NA
Tropical Japonica	504	33.70%	66.30%	0.00%	0.00%	NA
Japonica Intermediate	241	19.90%	79.70%	0.41%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	1.11%	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
vg0811308449	T -> C	LOC_Os08g18950.1	upstream_gene_variant ; 3841.0bp to feature; MODIFIER	silent_mutation	Average:59.928; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811308449	T -> C	LOC_Os08g18960.1	upstream_gene_variant ; 154.0bp to feature; MODIFIER	silent_mutation	Average:59.928; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811308449	T -> C	LOC_Os08g18970.1	upstream_gene_variant ; 2231.0bp to feature; MODIFIER	silent_mutation	Average:59.928; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811308449	T -> C	LOC_Os08g18960-LOC_Os08g18970	intergenic_region ; MODIFIER	silent_mutation	Average:59.928; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811308449	NA	5.70E-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
vg0811308449	NA	2.08E-31	mr1074	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
vg0811308449	6.16E-06	NA	mr1134	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
vg0811308449	NA	1.02E-06	mr1134	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
vg0811308449	3.45E-06	2.19E-76	mr1135	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
vg0811308449	NA	7.20E-21	mr1217	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
vg0811308449	NA	3.57E-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
vg0811308449	6.21E-06	7.60E-85	mr1504	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
vg0811308449	NA	9.05E-07	mr1504	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
vg0811308449	NA	1.97E-07	mr1659	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
vg0811308449	NA	3.68E-08	mr1660	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
vg0811308449	NA	6.69E-34	mr1670	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
vg0811308449	7.83E-07	5.38E-86	mr1672	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
vg0811308449	NA	4.46E-07	mr1672	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
vg0811308449	NA	8.73E-10	mr1714	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
vg0811308449	NA	5.61E-06	mr1835	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
vg0811308449	NA	1.69E-10	mr1595_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
vg0811308449	NA	5.67E-06	mr1672_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