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Detailed information for vg1124843037:

Variant ID: vg1124843037 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24843037
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTCTTCCCATTGGCAGCGACACCACCCGCCTCTCACCGCCCGCTCCCACCCTTTAGCTTCCGTAGTTGGCGGCGCGGCCCGCTCGCCGAGCCCGATGC[C/T]
GCCCGTCGCCGGCAGCTCGCCAAGGGGAGGAAGTGAGATAGGAGAGGAAGAGGTTATAGGAGGGGAGAGGAAGAGAGAGCGAGGAGGAGAGGTGAAAAAA

Reverse complement sequence

TTTTTTCACCTCTCCTCCTCGCTCTCTCTTCCTCTCCCCTCCTATAACCTCTTCCTCTCCTATCTCACTTCCTCCCCTTGGCGAGCTGCCGGCGACGGGC[G/A]
GCATCGGGCTCGGCGAGCGGGCCGCGCCGCCAACTACGGAAGCTAAAGGGTGGGAGCGGGCGGTGAGAGGCGGGTGGTGTCGCTGCCAATGGGAAGAGGA

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	70.90%	28.40%	0.17%	0.53%	NA
All Indica	2759	58.50%	41.10%	0.22%	0.25%	NA
All Japonica	1512	95.00%	5.00%	0.00%	0.07%	NA
Aus	269	56.50%	42.80%	0.00%	0.74%	NA
Indica I	595	66.40%	33.30%	0.17%	0.17%	NA
Indica II	465	74.60%	24.90%	0.22%	0.22%	NA
Indica III	913	38.90%	60.90%	0.11%	0.11%	NA
Indica Intermediate	786	65.60%	33.50%	0.38%	0.51%	NA
Temperate Japonica	767	97.10%	2.90%	0.00%	0.00%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	7.90%	0.00%	0.41%	NA
VI/Aromatic	96	82.30%	5.20%	1.04%	11.46%	NA
Intermediate	90	81.10%	13.30%	1.11%	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
vg1124843037	C -> T	LOC_Os11g41400.1	downstream_gene_variant ; 1001.0bp to feature; MODIFIER	silent_mutation	Average:70.514; most accessible tissue: Zhenshan97 young leaf, score: 84.624	N	N	N	N
vg1124843037	C -> T	LOC_Os11g41410.1	downstream_gene_variant ; 4375.0bp to feature; MODIFIER	silent_mutation	Average:70.514; most accessible tissue: Zhenshan97 young leaf, score: 84.624	N	N	N	N
vg1124843037	C -> T	LOC_Os11g41390.1	intron_variant ; MODIFIER	silent_mutation	Average:70.514; most accessible tissue: Zhenshan97 young leaf, score: 84.624	N	N	N	N
vg1124843037	C -> DEL	N	N	silent_mutation	Average:70.514; most accessible tissue: Zhenshan97 young leaf, score: 84.624	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124843037	4.35E-06	1.68E-08	mr1133	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
vg1124843037	NA	3.61E-06	mr1133_2	Ind_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
vg1124843037	NA	2.06E-06	mr1667_2	Ind_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