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Detailed information for vg1005877282:

Variant ID: vg1005877282 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5877282
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTACCAGCAAATTCTATTTATACTTGGGTTCAATTAGAACAAAAATTTCATGATCATTTTTGCACTGGTAAAACTGAGCTTAGGTTGTCTAATTTAA[C/T]
ATCTGTTAGGCAAAAATACAATGAATCTGTCGTTGATTATATTGAAAGGTTTAGAGATGTTAAAAGCTGATGTTTTAGTTTGAAAATAACTGACAAAGAT

Reverse complement sequence

ATCTTTGTCAGTTATTTTCAAACTAAAACATCAGCTTTTAACATCTCTAAACCTTTCAATATAATCAACGACAGATTCATTGTATTTTTGCCTAACAGAT[G/A]
TTAAATTAGACAACCTAAGCTCAGTTTTACCAGTGCAAAAATGATCATGAAATTTTTGTTCTAATTGAACCCAAGTATAAATAGAATTTGCTGGTAAAGA

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	90.40%	8.40%	1.16%	0.06%	NA
All Indica	2759	90.30%	9.00%	0.76%	0.00%	NA
All Japonica	1512	88.00%	9.70%	2.05%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	96.10%	2.60%	1.29%	0.00%	NA
Indica III	913	80.10%	19.40%	0.55%	0.00%	NA
Indica Intermediate	786	91.70%	7.10%	1.15%	0.00%	NA
Temperate Japonica	767	81.20%	18.80%	0.00%	0.00%	NA
Tropical Japonica	504	93.10%	0.20%	6.15%	0.60%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg1005877282	C -> T	LOC_Os10g10630.1	upstream_gene_variant ; 2377.0bp to feature; MODIFIER	silent_mutation	Average:27.488; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1005877282	C -> T	LOC_Os10g10640.1	intron_variant ; MODIFIER	silent_mutation	Average:27.488; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1005877282	C -> DEL	N	N	silent_mutation	Average:27.488; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005877282	NA	6.58E-07	mr1062	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
vg1005877282	1.99E-06	NA	mr1821_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