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Detailed information for vg1009640159:

Variant ID: vg1009640159 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9640159
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTGCTCGTCCCGAGTGAAGGCTATGGACTCTACAACAGAATTATGACTTCCTTACTTCCTTACTAATAGTCACGCAAACAAATTATTCAAAGTCATA[C/T]
TTGTATTTGTGGATGTTTGTAGTGTCTACCATGCAATCCTGAGCAATTGAGAAATGGAACAATCTTCACTAAGTCACCCTAACTTTTCATGAAGAACAAC

Reverse complement sequence

GTTGTTCTTCATGAAAAGTTAGGGTGACTTAGTGAAGATTGTTCCATTTCTCAATTGCTCAGGATTGCATGGTAGACACTACAAACATCCACAAATACAA[G/A]
TATGACTTTGAATAATTTGTTTGCGTGACTATTAGTAAGGAAGTAAGGAAGTCATAATTCTGTTGTAGAGTCCATAGCCTTCACTCGGGACGAGCAAAGG

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	42.50%	25.20%	0.44%	31.89%	NA
All Indica	2759	56.70%	5.70%	0.29%	37.33%	NA
All Japonica	1512	24.10%	45.80%	0.79%	29.37%	NA
Aus	269	11.90%	86.20%	0.37%	1.49%	NA
Indica I	595	72.60%	3.50%	0.50%	23.36%	NA
Indica II	465	40.60%	3.70%	0.22%	55.48%	NA
Indica III	913	61.10%	4.40%	0.00%	34.50%	NA
Indica Intermediate	786	49.00%	10.10%	0.51%	40.46%	NA
Temperate Japonica	767	17.30%	55.30%	1.04%	26.34%	NA
Tropical Japonica	504	22.80%	33.70%	0.60%	42.86%	NA
Japonica Intermediate	241	48.10%	40.70%	0.41%	10.79%	NA
VI/Aromatic	96	19.80%	79.20%	0.00%	1.04%	NA
Intermediate	90	33.30%	35.60%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009640159	C -> T	LOC_Os10g18930.1	upstream_gene_variant ; 1713.0bp to feature; MODIFIER	silent_mutation	Average:30.243; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg1009640159	C -> T	LOC_Os10g18940.1	downstream_gene_variant ; 3612.0bp to feature; MODIFIER	silent_mutation	Average:30.243; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg1009640159	C -> T	LOC_Os10g18930-LOC_Os10g18940	intergenic_region ; MODIFIER	silent_mutation	Average:30.243; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg1009640159	C -> DEL	N	N	silent_mutation	Average:30.243; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009640159	2.65E-06	NA	mr1291	Ind_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
vg1009640159	3.80E-06	6.95E-06	mr1471	Ind_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
vg1009640159	NA	9.20E-06	mr1732	Ind_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