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Detailed information for vg1012236072:

Variant ID: vg1012236072 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12236072
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, C: 0.13, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTCTCCTTTCCCCCACACCAGAGTTAAAGTTCTTCTGAGATGGAGCCATCTCAGAGAGGTTGGTTTCGTCGCTGCCGTCAAGGATTGCCTGTGGAATG[C/G]
AATCGCCCGCTGCAGGAGTCAAGTCTTCAGGCTTAGCTCGCTTTTATCTTTTCCGCTGCATTTGTAATCTTTTATATTTTTGTAAGATGTGGATCTGTAT

Reverse complement sequence

ATACAGATCCACATCTTACAAAAATATAAAAGATTACAAATGCAGCGGAAAAGATAAAAGCGAGCTAAGCCTGAAGACTTGACTCCTGCAGCGGGCGATT[G/C]
CATTCCACAGGCAATCCTTGACGGCAGCGACGAAACCAACCTCTCTGAGATGGCTCCATCTCAGAAGAACTTTAACTCTGGTGTGGGGGAAAGGAGAACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.10%	17.80%	1.42%	49.62%	NA
All Indica	2759	2.60%	28.60%	0.91%	67.85%	NA
All Japonica	1512	89.30%	0.40%	0.13%	10.19%	NA
Aus	269	1.10%	9.70%	9.67%	79.55%	NA
Indica I	595	3.90%	7.40%	1.34%	87.39%	NA
Indica II	465	3.70%	35.90%	0.65%	59.78%	NA
Indica III	913	1.00%	33.60%	0.77%	64.62%	NA
Indica Intermediate	786	2.90%	34.60%	0.89%	61.58%	NA
Temperate Japonica	767	97.00%	0.30%	0.00%	2.74%	NA
Tropical Japonica	504	81.90%	0.40%	0.20%	17.46%	NA
Japonica Intermediate	241	80.10%	0.80%	0.41%	18.67%	NA
VI/Aromatic	96	9.40%	3.10%	13.54%	73.96%	NA
Intermediate	90	41.10%	20.00%	1.11%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012236072	C -> G	LOC_Os10g23860.1	downstream_gene_variant ; 960.0bp to feature; MODIFIER	silent_mutation	Average:19.21; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1012236072	C -> G	LOC_Os10g23870.1	downstream_gene_variant ; 3392.0bp to feature; MODIFIER	silent_mutation	Average:19.21; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1012236072	C -> G	LOC_Os10g23840-LOC_Os10g23860	intergenic_region ; MODIFIER	silent_mutation	Average:19.21; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1012236072	C -> DEL	N	N	silent_mutation	Average:19.21; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012236072	NA	9.01E-06	mr1100	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
vg1012236072	NA	3.36E-07	mr1162	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
vg1012236072	5.26E-06	2.19E-06	mr1613	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
vg1012236072	8.32E-06	3.98E-06	mr1619	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
vg1012236072	9.93E-09	9.93E-09	mr1795	Jap_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
vg1012236072	NA	5.02E-11	mr1819	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
vg1012236072	NA	4.77E-08	mr1576_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