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Detailed information for vg0715810096:

Variant ID: vg0715810096 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15810096
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGAGAACCCAAGCTATTATTTTGAGGGCGTCGTGGAGGGTTCAAACATCTACACCAAGGACACGGTAGATGATCTCGATGACAAGCAAGGTCAAGGTTT[T/C]
ATGTCGGCCGATGATTTGGAAGAAATAGATATAGGTCCAGGCGATCGGCGGAGGCCGACATTTATTAGTAAGAACTTATCTCCAGAGTTTAGAACCAAGC

Reverse complement sequence

GCTTGGTTCTAAACTCTGGAGATAAGTTCTTACTAATAAATGTCGGCCTCCGCCGATCGCCTGGACCTATATCTATTTCTTCCAAATCATCGGCCGACAT[A/G]
AAACCTTGACCTTGCTTGTCATCGAGATCATCTACCGTGTCCTTGGTGTAGATGTTTGAACCCTCCACGACGCCCTCAAAATAATAGCTTGGGTTCTCCA

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	64.10%	35.80%	0.11%	0.00%	NA
All Indica	2759	95.70%	4.10%	0.14%	0.00%	NA
All Japonica	1512	6.70%	93.30%	0.00%	0.00%	NA
Aus	269	86.60%	13.40%	0.00%	0.00%	NA
Indica I	595	98.20%	1.70%	0.17%	0.00%	NA
Indica II	465	94.80%	4.90%	0.22%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	90.60%	9.20%	0.25%	0.00%	NA
Temperate Japonica	767	11.50%	88.50%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715810096	T -> C	LOC_Os07g27200.1	synonymous_variant ; p.Phe1217Phe; LOW	synonymous_codon	Average:32.476; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715810096	6.45E-07	1.85E-06	mr1510	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
vg0715810096	NA	2.28E-08	mr1004_2	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