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Detailed information for vg1009046745:

Variant ID: vg1009046745 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9046745
Reference Allele: C	Alternative Allele: T,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATCTTCAACGCATGAACCACTGCAGCTAATTCAAGATCATGAGTAGGGTAGTTCTTCTCATGCGGACGTAACTGATGAGATGCGTAGGCAACCACCTT[C/T,G]
CCATCTTGCATCAGAACACATCCTAACCCAAGCTTAGATGCATCGCAATACACTTGGAAACCCTTCTTTGGATCAGGCAAAATCAAGATGGGTGCTGATA

Reverse complement sequence

TATCAGCACCCATCTTGATTTTGCCTGATCCAAAGAAGGGTTTCCAAGTGTATTGCGATGCATCTAAGCTTGGGTTAGGATGTGTTCTGATGCAAGATGG[G/A,C]
AAGGTGGTTGCCTACGCATCTCATCAGTTACGTCCGCATGAGAAGAACTACCCTACTCATGATCTTGAATTAGCTGCAGTGGTTCATGCGTTGAAGATTT

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	49.20%	0.50%	35.10%	14.85%	G: 0.30%
All Indica	2759	45.70%	0.80%	41.32%	11.67%	G: 0.51%
All Japonica	1512	62.00%	0.10%	17.92%	19.97%	NA
Aus	269	6.30%	0.00%	72.12%	21.56%	NA
Indica I	595	44.50%	0.50%	40.50%	14.45%	NA
Indica II	465	34.60%	1.30%	49.68%	14.41%	NA
Indica III	913	57.10%	0.50%	34.72%	6.13%	G: 1.53%
Indica Intermediate	786	39.80%	1.10%	44.66%	14.38%	NA
Temperate Japonica	767	77.10%	0.00%	3.26%	19.69%	NA
Tropical Japonica	504	38.10%	0.20%	39.68%	22.02%	NA
Japonica Intermediate	241	64.30%	0.00%	19.09%	16.60%	NA
VI/Aromatic	96	58.30%	0.00%	29.17%	12.50%	NA
Intermediate	90	62.20%	0.00%	28.89%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009046745	C -> G	LOC_Os10g17900.1	synonymous_variant ; p.Gly1113Gly; LOW	synonymous_codon	Average:15.003; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1009046745	C -> T	LOC_Os10g17900.1	synonymous_variant ; p.Gly1113Gly; LOW	synonymous_codon	Average:15.003; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1009046745	C -> DEL	LOC_Os10g17900.1	N	frameshift_variant	Average:15.003; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009046745	4.39E-06	4.38E-06	mr1184	Jap_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