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Detailed information for vg1124903385:

Variant ID: vg1124903385 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24903385
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

ACATATTTTGCATGTGTTGGACGAAAATGCCCTCATCTTCTACGTCTCTTCTTTCATCTTCTACCTCTCTCTTCCCAAATCCTGTCACCGGCGATGTCCG[C/T]
TGCGGGAGCTCGGAGCGCCGGATAGAACACCGCAGGTCCGCCATCCACCGAGGCTCTTCACGAAGGCCGTCCTCTGCTACGTCGGGGTTCGAGGCAGTCA

Reverse complement sequence

TGACTGCCTCGAACCCCGACGTAGCAGAGGACGGCCTTCGTGAAGAGCCTCGGTGGATGGCGGACCTGCGGTGTTCTATCCGGCGCTCCGAGCTCCCGCA[G/A]
CGGACATCGCCGGTGACAGGATTTGGGAAGAGAGAGGTAGAAGATGAAAGAAGAGACGTAGAAGATGAGGGCATTTTCGTCCAACACATGCAAAATATGT

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	46.90%	45.20%	0.55%	7.41%	NA
All Indica	2759	33.80%	54.20%	0.51%	11.49%	NA
All Japonica	1512	62.60%	35.40%	0.20%	1.79%	NA
Aus	269	77.00%	19.70%	2.60%	0.74%	NA
Indica I	595	12.90%	66.20%	0.17%	20.67%	NA
Indica II	465	25.80%	71.40%	0.43%	2.37%	NA
Indica III	913	50.80%	33.70%	0.33%	15.12%	NA
Indica Intermediate	786	34.60%	58.70%	1.02%	5.73%	NA
Temperate Japonica	767	85.80%	14.20%	0.00%	0.00%	NA
Tropical Japonica	504	42.10%	52.40%	0.40%	5.16%	NA
Japonica Intermediate	241	32.00%	67.20%	0.41%	0.41%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	46.70%	46.70%	2.22%	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
vg1124903385	C -> T	LOC_Os11g41510.1	upstream_gene_variant ; 3959.0bp to feature; MODIFIER	silent_mutation	Average:49.212; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg1124903385	C -> T	LOC_Os11g41520.1	downstream_gene_variant ; 363.0bp to feature; MODIFIER	silent_mutation	Average:49.212; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg1124903385	C -> T	LOC_Os11g41530.1	downstream_gene_variant ; 3517.0bp to feature; MODIFIER	silent_mutation	Average:49.212; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg1124903385	C -> T	LOC_Os11g41520-LOC_Os11g41530	intergenic_region ; MODIFIER	silent_mutation	Average:49.212; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg1124903385	C -> DEL	N	N	silent_mutation	Average:49.212; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124903385	NA	7.23E-08	mr1045	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
vg1124903385	NA	4.58E-07	mr1330	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
vg1124903385	NA	6.60E-07	mr1579	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
vg1124903385	7.66E-07	7.66E-07	mr1701	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
vg1124903385	NA	3.56E-06	mr1871	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
vg1124903385	NA	2.02E-07	mr1042_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
vg1124903385	1.83E-07	1.83E-07	mr1579_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
vg1124903385	NA	2.84E-06	mr1680_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
vg1124903385	NA	6.63E-09	mr1871_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