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Detailed information for vg0812629955:

Variant ID: vg0812629955 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12629955
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GGATTGTATTACCAGTAGGAAGTTGAATCTGTTTCTCCCGAAGTAACAAATCAAAAATCTTATCAGCCTTGATGATATCAAAGTCATACCTCTCTTCTTT[T/C]
CCAGAACTCTTCACCCATTGGCATGGTATAACCTTCTTGTTTCTAACCCATTCGGCTGCTGCTATTTCGGAGTCGTCATCATCATCATCATCATCTGATC

Reverse complement sequence

GATCAGATGATGATGATGATGATGACGACTCCGAAATAGCAGCAGCCGAATGGGTTAGAAACAAGAAGGTTATACCATGCCAATGGGTGAAGAGTTCTGG[A/G]
AAAGAAGAGAGGTATGACTTTGATATCATCAAGGCTGATAAGATTTTTGATTTGTTACTTCGGGAGAAACAGATTCAACTTCCTACTGGTAATACAATCC

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	96.70%	0.90%	1.63%	0.83%	NA
All Indica	2759	99.80%	0.00%	0.11%	0.04%	NA
All Japonica	1512	90.40%	2.50%	4.70%	2.38%	NA
Aus	269	98.50%	0.40%	0.74%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.25%	0.13%	NA
Temperate Japonica	767	99.30%	0.40%	0.13%	0.13%	NA
Tropical Japonica	504	76.40%	5.80%	11.11%	6.75%	NA
Japonica Intermediate	241	91.30%	2.50%	5.81%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812629955	T -> C	LOC_Os08g21124.1	synonymous_variant ; p.Gly292Gly; LOW	synonymous_codon	Average:48.222; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N
vg0812629955	T -> DEL	LOC_Os08g21124.1	N	frameshift_variant	Average:48.222; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812629955	8.05E-07	2.69E-11	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
vg0812629955	NA	1.86E-07	mr1951	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
vg0812629955	NA	2.41E-06	mr1557_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
vg0812629955	NA	5.30E-07	mr1562_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
vg0812629955	NA	2.22E-07	mr1696_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
vg0812629955	NA	8.20E-11	mr1769_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
vg0812629955	NA	3.39E-08	mr1819_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
vg0812629955	NA	7.74E-07	mr1849_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
vg0812629955	4.11E-06	6.65E-13	mr1905_2	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
vg0812629955	NA	3.41E-07	mr1905_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
vg0812629955	NA	9.36E-10	mr1916_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
vg0812629955	NA	5.69E-06	mr1944_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