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Detailed information for vg1124841437:

Variant ID: vg1124841437 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24841437
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCTGGTGCTGGCGTGGCGTGTTAGAGCTGATGAAGCCAGTTAGCGCGTGTTGCGGCAAGATAGATAGAAACGGATTAGCCGGTTAGTTTGTTTCCTTTC[C/T]
GATTAAACTTTTCCATATTTTTGTGGGATCAATTAGGATTGTTAAAGATTGATTAGAGTGACCAGTATATATACTGGTGACGATAGATTAGAGAAGGCCC

Reverse complement sequence

GGGCCTTCTCTAATCTATCGTCACCAGTATATATACTGGTCACTCTAATCAATCTTTAACAATCCTAATTGATCCCACAAAAATATGGAAAAGTTTAATC[G/A]
GAAAGGAAACAAACTAACCGGCTAATCCGTTTCTATCTATCTTGCCGCAACACGCGCTAACTGGCTTCATCAGCTCTAACACGCCACGCCAGCACCAGCA

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	84.00%	15.50%	0.49%	0.00%	NA
All Indica	2759	97.50%	2.40%	0.11%	0.00%	NA
All Japonica	1512	62.80%	37.00%	0.20%	0.00%	NA
Aus	269	85.50%	13.80%	0.74%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	96.10%	3.90%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.70%	0.38%	0.00%	NA
Temperate Japonica	767	87.40%	12.60%	0.00%	0.00%	NA
Tropical Japonica	504	34.10%	65.50%	0.40%	0.00%	NA
Japonica Intermediate	241	44.80%	54.80%	0.41%	0.00%	NA
VI/Aromatic	96	29.20%	58.30%	12.50%	0.00%	NA
Intermediate	90	81.10%	15.60%	3.33%	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
vg1124841437	C -> T	LOC_Os11g41380.1	downstream_gene_variant ; 4645.0bp to feature; MODIFIER	silent_mutation	Average:46.103; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1124841437	C -> T	LOC_Os11g41400.1	downstream_gene_variant ; 2601.0bp to feature; MODIFIER	silent_mutation	Average:46.103; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1124841437	C -> T	LOC_Os11g41390.1	intron_variant ; MODIFIER	silent_mutation	Average:46.103; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124841437	NA	5.45E-12	mr1609	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
vg1124841437	NA	5.98E-06	mr1195_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
vg1124841437	6.95E-07	NA	mr1238_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
vg1124841437	NA	3.13E-10	mr1398_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
vg1124841437	5.03E-06	NA	mr1484_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
vg1124841437	NA	3.93E-07	mr1554_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
vg1124841437	NA	7.77E-08	mr1582_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
vg1124841437	8.96E-07	NA	mr1609_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
vg1124841437	1.20E-06	1.20E-06	mr1609_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
vg1124841437	NA	1.92E-06	mr1730_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
vg1124841437	2.44E-06	NA	mr1841_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
vg1124841437	3.61E-07	NA	mr1900_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
vg1124841437	NA	6.70E-06	mr1959_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