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Detailed information for vg1013060158:

Variant ID: vg1013060158 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13060158
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGGTAGGCTGGGCGTTTGCTCGACCATGTCGAGGCTCCGCTTGTCGCATTGTACCAAAAGTTTTGCATTCCCTTGAATAGTGATTGTTCCCTTCGGTCC[C/T]
GGCATCTTGAGCACTTGATACGCGTAGTGAGATACGGCCATGAACTTCGCAAGTGCAGTTCTCCCGATGATGGCGTTAACGCTGTATCGAATTCAGCGAC

Reverse complement sequence

GTCGCTGAATTCGATACAGCGTTAACGCCATCATCGGGAGAACTGCACTTGCGAAGTTCATGGCCGTATCTCACTACGCGTATCAAGTGCTCAAGATGCC[G/A]
GGACCGAAGGGAACAATCACTATTCAAGGGAATGCAAAACTTTTGGTACAATGCGACAAGCGGAGCCTCGACATGGTCGAGCAAACGCCCAGCCTACCCG

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	88.60%	11.20%	0.00%	0.30%	NA
All Indica	2759	81.50%	18.10%	0.00%	0.47%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	89.20%	10.60%	0.00%	0.17%	NA
Indica II	465	92.30%	7.50%	0.00%	0.22%	NA
Indica III	913	75.70%	23.70%	0.00%	0.66%	NA
Indica Intermediate	786	76.00%	23.40%	0.00%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013060158	C -> T	LOC_Os10g25280.1	synonymous_variant ; p.Pro792Pro; LOW	synonymous_codon	Average:49.14; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg1013060158	C -> DEL	LOC_Os10g25280.1	N	frameshift_variant	Average:49.14; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013060158	8.33E-06	NA	mr1003	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
vg1013060158	4.37E-06	NA	mr1051	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