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Detailed information for vg0527080981:

Variant ID: vg0527080981 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27080981
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.26, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CTCACAGGAACCAACCATATAAAAAATAAACTCAAACGGACGAAATATATAACATGTGGAATTTTCCAAAGCTCTACCGAAAAACTTCTCTCCTCGAAAA[T/C]
ACAATCTTGCAAGCGGAATTTGGAGGTTTTAATATCGCCGAACCCGGCGAAGCAGGGAGAATCGGATGTAACTTTTTCTGTAGATGTCCGTGCATATATT

Reverse complement sequence

AATATATGCACGGACATCTACAGAAAAAGTTACATCCGATTCTCCCTGCTTCGCCGGGTTCGGCGATATTAAAACCTCCAAATTCCGCTTGCAAGATTGT[A/G]
TTTTCGAGGAGAGAAGTTTTTCGGTAGAGCTTTGGAAAATTCCACATGTTATATATTTCGTCCGTTTGAGTTTATTTTTTATATGGTTGGTTCCTGTGAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	21.80%	6.80%	51.29%	20.08%	NA
All Indica	2759	2.40%	10.50%	60.24%	26.86%	NA
All Japonica	1512	58.10%	1.20%	31.08%	9.59%	NA
Aus	269	14.90%	1.50%	71.75%	11.90%	NA
Indica I	595	1.50%	18.70%	37.65%	42.18%	NA
Indica II	465	2.60%	9.00%	58.06%	30.32%	NA
Indica III	913	2.40%	8.10%	74.26%	15.22%	NA
Indica Intermediate	786	2.90%	8.00%	62.34%	26.72%	NA
Temperate Japonica	767	95.30%	0.10%	4.04%	0.52%	NA
Tropical Japonica	504	5.00%	3.00%	73.81%	18.25%	NA
Japonica Intermediate	241	51.00%	0.80%	27.80%	20.33%	NA
VI/Aromatic	96	20.80%	2.10%	64.58%	12.50%	NA
Intermediate	90	28.90%	8.90%	41.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0527080981	T -> DEL	N	N	silent_mutation	Average:12.104; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0527080981	T -> C	LOC_Os05g46760.1	upstream_gene_variant ; 3616.0bp to feature; MODIFIER	silent_mutation	Average:12.104; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0527080981	T -> C	LOC_Os05g46770.1	upstream_gene_variant ; 4251.0bp to feature; MODIFIER	silent_mutation	Average:12.104; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0527080981	T -> C	LOC_Os05g46770.2	upstream_gene_variant ; 4251.0bp to feature; MODIFIER	silent_mutation	Average:12.104; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0527080981	T -> C	LOC_Os05g46760-LOC_Os05g46770	intergenic_region ; MODIFIER	silent_mutation	Average:12.104; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527080981	NA	1.45E-12	mr1194	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
vg0527080981	2.96E-06	2.96E-06	mr1782	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
vg0527080981	NA	1.38E-07	mr1194_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
vg0527080981	NA	2.12E-06	mr1715_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