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Detailed information for vg1010774180:

Variant ID: vg1010774180 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10774180
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAAGAAATGTTTCCGCCTTTTTATCAAGCAAGTCCAACCTATCTAAAATCTCCTTTCTTTTTTTTTGTGCAAACCACTTGTATGTTTAGCCCAACCC[T/C]
TGAGATGTTGTCTAAATCGACGAATTTTCGCCTGCCAACGTTCCATAGGAGAATTTCCTTCATCAACACTAGAACAAACTTCCTTCACCATATCAACAAA

Reverse complement sequence

TTTGTTGATATGGTGAAGGAAGTTTGTTCTAGTGTTGATGAAGGAAATTCTCCTATGGAACGTTGGCAGGCGAAAATTCGTCGATTTAGACAACATCTCA[A/G]
GGGTTGGGCTAAACATACAAGTGGTTTGCACAAAAAAAAAGAAAGGAGATTTTAGATAGGTTGGACTTGCTTGATAAAAAGGCGGAAACATTTCTTTTGA

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	90.00%	5.30%	0.15%	4.51%	NA
All Indica	2759	96.00%	0.30%	0.00%	3.66%	NA
All Japonica	1512	76.80%	15.70%	0.20%	7.28%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	90.10%	0.20%	0.00%	9.75%	NA
Indica II	465	98.90%	0.40%	0.00%	0.65%	NA
Indica III	913	98.70%	0.00%	0.00%	1.31%	NA
Indica Intermediate	786	95.70%	0.80%	0.00%	3.56%	NA
Temperate Japonica	767	57.20%	28.30%	0.26%	14.21%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	4.40%	1.11%	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
vg1010774180	T -> C	LOC_Os10g21150.1	downstream_gene_variant ; 2954.0bp to feature; MODIFIER	silent_mutation	Average:33.747; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg1010774180	T -> C	LOC_Os10g21150-LOC_Os10g21160	intergenic_region ; MODIFIER	silent_mutation	Average:33.747; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg1010774180	T -> DEL	N	N	silent_mutation	Average:33.747; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010774180	NA	2.97E-06	mr1354_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
vg1010774180	2.01E-06	1.90E-09	mr1645_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
vg1010774180	7.80E-07	6.09E-08	mr1647_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
vg1010774180	6.96E-06	6.96E-06	mr1647_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
vg1010774180	NA	7.58E-09	mr1660_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