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Detailed information for vg1124026265:

Variant ID: vg1124026265 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24026265
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, C: 0.33, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGGCAGCGAAGGGCAAATGGCCAGAGGAGATGCTATCTGTTCTCTGGGCCCTTCGAACGACCCCCACAAGACCAACCAAGTTCAGCCCGTTCATGCTT[A/C]
TTTATGGCGATGAGGCAATGACCCCGACAGAGCTAGGGGCTAACTCACCAAGGGTGATGTTCTCTGGGGACGAAGAGGGGCGCGAGGTGTCGCTCGAACT

Reverse complement sequence

AGTTCGAGCGACACCTCGCGCCCCTCTTCGTCCCCAGAGAACATCACCCTTGGTGAGTTAGCCCCTAGCTCTGTCGGGGTCATTGCCTCATCGCCATAAA[T/G]
AAGCATGAACGGGCTGAACTTGGTTGGTCTTGTGGGGGTCGTTCGAAGGGCCCAGAGAACAGATAGCATCTCCTCTGGCCATTTGCCCTTCGCTGCCCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	31.30%	5.37%	13.22%	NA
All Indica	2759	67.50%	25.20%	4.75%	2.57%	NA
All Japonica	1512	16.00%	43.00%	5.95%	35.05%	NA
Aus	269	53.50%	34.20%	7.81%	4.46%	NA
Indica I	595	63.00%	14.60%	14.29%	8.07%	NA
Indica II	465	69.00%	27.70%	2.37%	0.86%	NA
Indica III	913	73.90%	24.90%	1.10%	0.11%	NA
Indica Intermediate	786	62.60%	31.90%	3.18%	2.29%	NA
Temperate Japonica	767	6.00%	57.20%	6.91%	29.86%	NA
Tropical Japonica	504	27.20%	32.10%	4.96%	35.71%	NA
Japonica Intermediate	241	24.50%	20.30%	4.98%	50.21%	NA
VI/Aromatic	96	81.20%	5.20%	6.25%	7.29%	NA
Intermediate	90	43.30%	44.40%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124026265	A -> DEL	N	N	silent_mutation	Average:16.024; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1124026265	A -> C	LOC_Os11g40284.1	3_prime_UTR_variant ; 919.0bp to feature; MODIFIER	silent_mutation	Average:16.024; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1124026265	A -> C	LOC_Os11g40300.1	downstream_gene_variant ; 1731.0bp to feature; MODIFIER	silent_mutation	Average:16.024; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124026265	NA	5.39E-06	mr1153_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
vg1124026265	NA	2.86E-06	mr1407_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
vg1124026265	4.78E-06	5.01E-09	mr1606_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