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Detailed information for vg1125299435:

Variant ID: vg1125299435 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25299435
Reference Allele: T	Alternative Allele: C,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAACGGTGGCCATACCCCATCTTGGAAGTGGGCCCAACCACACGAGGCCCTCAATCCCCTAAGAGCAGGTACAATAGCAGGCTATAAGCCAGCTATAAA[T/C,G]
ACATTTTAAGAAGATAAAAGATAAGAGAGAAGGACAGCGAGCTATAGATTTGTAGCCAGCTATAGTATGGACTCCAAAGTGCATATGTGTATGACAGATG

Reverse complement sequence

CATCTGTCATACACATATGCACTTTGGAGTCCATACTATAGCTGGCTACAAATCTATAGCTCGCTGTCCTTCTCTCTTATCTTTTATCTTCTTAAAATGT[A/G,C]
TTTATAGCTGGCTTATAGCCTGCTATTGTACCTGCTCTTAGGGGATTGAGGGCCTCGTGTGGTTGGGCCCACTTCCAAGATGGGGTATGGCCACCGTTGG

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	55.90%	5.40%	2.35%	36.33%	G: 0.02%
All Indica	2759	73.30%	0.20%	0.76%	25.77%	G: 0.04%
All Japonica	1512	27.80%	16.30%	5.16%	50.66%	NA
Aus	269	36.80%	0.70%	2.60%	59.85%	NA
Indica I	595	46.10%	0.30%	2.02%	51.60%	NA
Indica II	465	64.90%	0.20%	0.43%	34.41%	NA
Indica III	913	90.70%	0.00%	0.00%	9.20%	G: 0.11%
Indica Intermediate	786	78.50%	0.30%	0.89%	20.36%	NA
Temperate Japonica	767	19.40%	29.30%	8.21%	43.02%	NA
Tropical Japonica	504	39.50%	1.00%	1.59%	57.94%	NA
Japonica Intermediate	241	30.30%	7.10%	2.90%	59.75%	NA
VI/Aromatic	96	53.10%	1.00%	1.04%	44.79%	NA
Intermediate	90	54.40%	1.10%	4.44%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125299435	T -> DEL	N	N	silent_mutation	Average:47.951; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125299435	T -> G	LOC_Os11g42050.1	upstream_gene_variant ; 2615.0bp to feature; MODIFIER	silent_mutation	Average:47.951; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125299435	T -> G	LOC_Os11g42050-LOC_Os11g42060	intergenic_region ; MODIFIER	silent_mutation	Average:47.951; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125299435	T -> C	LOC_Os11g42050.1	upstream_gene_variant ; 2615.0bp to feature; MODIFIER	silent_mutation	Average:47.951; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125299435	T -> C	LOC_Os11g42050-LOC_Os11g42060	intergenic_region ; MODIFIER	silent_mutation	Average:47.951; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125299435	1.82E-06	1.82E-06	mr1657_2	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