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Detailed information for vg0711716216:

Variant ID: vg0711716216 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11716216
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTAGCTGGGCTGAGAACAACAAAGCCGTTCGAAGGTCCTACTTACTACTAGTTACTGCACAGTGGGGTCTTGGTTCATCATAGTGGTCGAACTCTTGC[T/C]
AGGCCTAAGACAAGGTATCTATATCGTCACACTTTCATGAATCCCACTGTTGTGAAACACTGCCCCCTAACTCCTTACGCATGTTCACCCCAACCGCTCA

Reverse complement sequence

TGAGCGGTTGGGGTGAACATGCGTAAGGAGTTAGGGGGCAGTGTTTCACAACAGTGGGATTCATGAAAGTGTGACGATATAGATACCTTGTCTTAGGCCT[A/G]
GCAAGAGTTCGACCACTATGATGAACCAAGACCCCACTGTGCAGTAACTAGTAGTAAGTAGGACCTTCGAACGGCTTTGTTGTTCTCAGCCCAGCTAGCT

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	59.70%	25.60%	1.18%	13.58%	NA
All Indica	2759	86.10%	1.40%	0.72%	11.71%	NA
All Japonica	1512	6.50%	75.10%	0.73%	17.59%	NA
Aus	269	95.20%	0.00%	1.49%	3.35%	NA
Indica I	595	69.70%	1.80%	1.51%	26.89%	NA
Indica II	465	91.80%	3.00%	0.00%	5.16%	NA
Indica III	913	99.50%	0.10%	0.11%	0.33%	NA
Indica Intermediate	786	79.60%	1.80%	1.27%	17.30%	NA
Temperate Japonica	767	2.20%	67.00%	1.30%	29.47%	NA
Tropical Japonica	504	13.70%	85.70%	0.20%	0.40%	NA
Japonica Intermediate	241	5.40%	78.80%	0.00%	15.77%	NA
VI/Aromatic	96	38.50%	1.00%	18.75%	41.67%	NA
Intermediate	90	57.80%	34.40%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711716216	T -> DEL	N	N	silent_mutation	Average:41.889; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0711716216	T -> C	LOC_Os07g20300.1	downstream_gene_variant ; 2353.0bp to feature; MODIFIER	silent_mutation	Average:41.889; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0711716216	T -> C	LOC_Os07g20300-LOC_Os07g20310	intergenic_region ; MODIFIER	silent_mutation	Average:41.889; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711716216	NA	7.88E-12	mr1666_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
vg0711716216	NA	8.49E-06	mr1693_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
vg0711716216	NA	8.45E-17	mr1712_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
vg0711716216	7.96E-06	2.13E-16	mr1717_2	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