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Detailed information for vg1116393407:

Variant ID: vg1116393407 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16393407
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTGCATAAATCAAAATTTTTCTACCACGTAAACCAGTAACCATGTAAGTATTAGATCATAGATCGTTACCACTCGACGCGCTGTGTAGCAGAAGTAAG[T/C]
GCTAAGAAGCCGAAGAAATGTCAGGGATGTAGCGCGCGTCGATGTAGAGGAAGTAGTCGATCGCAACAGCTCAACCTTCTCCTCCTCGTGCGTTATCCTC

Reverse complement sequence

GAGGATAACGCACGAGGAGGAGAAGGTTGAGCTGTTGCGATCGACTACTTCCTCTACATCGACGCGCGCTACATCCCTGACATTTCTTCGGCTTCTTAGC[A/G]
CTTACTTCTGCTACACAGCGCGTCGAGTGGTAACGATCTATGATCTAATACTTACATGGTTACTGGTTTACGTGGTAGAAAAATTTTGATTTATGCAATC

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	71.90%	28.00%	0.06%	0.00%	NA
All Indica	2759	99.00%	1.00%	0.00%	0.00%	NA
All Japonica	1512	19.50%	80.40%	0.13%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	19.60%	80.20%	0.26%	0.00%	NA
Tropical Japonica	504	24.80%	75.20%	0.00%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	51.00%	49.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	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
vg1116393407	T -> C	LOC_Os11g28480.1	intron_variant ; MODIFIER	silent_mutation	Average:46.565; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116393407	1.87E-06	NA	mr1078_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
vg1116393407	NA	3.38E-06	mr1078_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
vg1116393407	NA	8.18E-15	mr1162_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
vg1116393407	NA	3.03E-06	mr1754_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
vg1116393407	NA	1.05E-14	mr1790_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