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Detailed information for vg1011062873:

Variant ID: vg1011062873 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11062873
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCACCGCCGCCAACCAGTTTCCTCGCTTACATGGTTAGTTCGTCACACCACCATTGTTGGGCATCTACACCTTTACCGCCGCCCGCCGTCATCACCGC[C/T]
GACCGGTTTCTTCGCCTCCACACGGTTGGTGTATTCCGCCGCCATTGCTGATGGTGACCATGTCCTCACTATCGGCTGTCGTCAACGCCTGTCACGTCCC

Reverse complement sequence

GGGACGTGACAGGCGTTGACGACAGCCGATAGTGAGGACATGGTCACCATCAGCAATGGCGGCGGAATACACCAACCGTGTGGAGGCGAAGAAACCGGTC[G/A]
GCGGTGATGACGGCGGGCGGCGGTAAAGGTGTAGATGCCCAACAATGGTGGTGTGACGAACTAACCATGTAAGCGAGGAAACTGGTTGGCGGCGGTGAAG

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	34.00%	18.70%	2.96%	44.31%	NA
All Indica	2759	26.90%	2.50%	1.27%	69.37%	NA
All Japonica	1512	34.90%	51.50%	6.28%	7.34%	NA
Aus	269	98.90%	0.40%	0.37%	0.37%	NA
Indica I	595	19.70%	5.70%	0.67%	73.95%	NA
Indica II	465	13.30%	1.90%	1.08%	83.66%	NA
Indica III	913	32.60%	0.90%	1.86%	64.62%	NA
Indica Intermediate	786	33.60%	2.30%	1.15%	62.98%	NA
Temperate Japonica	767	11.90%	82.00%	4.69%	1.43%	NA
Tropical Japonica	504	67.50%	7.30%	8.73%	16.47%	NA
Japonica Intermediate	241	39.80%	46.90%	6.22%	7.05%	NA
VI/Aromatic	96	37.50%	9.40%	6.25%	46.88%	NA
Intermediate	90	42.20%	28.90%	3.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011062873	C -> T	LOC_Os10g21600.1	downstream_gene_variant ; 2955.0bp to feature; MODIFIER	silent_mutation	Average:15.997; most accessible tissue: Callus, score: 47.472	N	N	N	N
vg1011062873	C -> T	LOC_Os10g21600-LOC_Os10g21620	intergenic_region ; MODIFIER	silent_mutation	Average:15.997; most accessible tissue: Callus, score: 47.472	N	N	N	N
vg1011062873	C -> DEL	N	N	silent_mutation	Average:15.997; most accessible tissue: Callus, score: 47.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011062873	2.08E-06	NA	mr1128	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
vg1011062873	NA	5.41E-08	mr1310	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
vg1011062873	NA	8.14E-08	mr1926	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
vg1011062873	NA	2.64E-09	mr1959	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
vg1011062873	NA	5.04E-07	mr1495_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