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Detailed information for vg1009049826:

Variant ID: vg1009049826 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9049826
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTTCTTTTTCCACCACACGGACCTTTGGCGCCAATTGGTAGCGAGGGACAAATAGAGCTCTCTTCCTTGCGGTAAGACGAATTCTGGCCTTCTGCGG[T/C]
GGTGCTTCTCCCTTCAATGCGGCTAGTTCCTTCTCCAAACGATCCACCTTGTCCTCTAACTTGCAAATCTTACCACGATTCCGGTCTTCACGATCTTGAG

Reverse complement sequence

CTCAAGATCGTGAAGACCGGAATCGTGGTAAGATTTGCAAGTTAGAGGACAAGGTGGATCGTTTGGAGAAGGAACTAGCCGCATTGAAGGGAGAAGCACC[A/G]
CCGCAGAAGGCCAGAATTCGTCTTACCGCAAGGAAGAGAGCTCTATTTGTCCCTCGCTACCAATTGGCGCCAAAGGTCCGTGTGGTGGAAAAAGAAGTTA

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	80.60%	0.10%	5.18%	14.13%	NA
All Indica	2759	92.40%	0.20%	3.26%	4.10%	NA
All Japonica	1512	56.50%	0.00%	9.72%	33.80%	NA
Aus	269	98.10%	0.00%	0.37%	1.49%	NA
Indica I	595	98.30%	0.20%	1.01%	0.50%	NA
Indica II	465	91.40%	0.60%	2.80%	5.16%	NA
Indica III	913	89.40%	0.00%	4.49%	6.13%	NA
Indica Intermediate	786	92.10%	0.30%	3.82%	3.82%	NA
Temperate Japonica	767	64.90%	0.00%	1.04%	34.03%	NA
Tropical Japonica	504	40.10%	0.00%	23.61%	36.31%	NA
Japonica Intermediate	241	63.90%	0.00%	8.30%	27.80%	NA
VI/Aromatic	96	63.50%	0.00%	2.08%	34.38%	NA
Intermediate	90	86.70%	0.00%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009049826	T -> C	LOC_Os10g17900.1	synonymous_variant ; p.Pro217Pro; LOW	synonymous_codon	Average:12.066; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1009049826	T -> DEL	LOC_Os10g17900.1	N	frameshift_variant	Average:12.066; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009049826	1.66E-07	3.85E-07	mr1730	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