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Detailed information for vg1127863155:

Variant ID: vg1127863155 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27863155
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGTACTTGTAGCTAGAATTCCAAAAACCACTCTTATCTTCATGCCCTCTCGCTTACGTGAGTCTTACTCGTACAGATCGCAAAATCAAATCCCAGGCT[T/C]
AATTCGATGTCTTAGTCAACAAAATCAAGAGGCTTGAAGGAGCTAGAGATGAAGTCGCCAATGCTGCTACACCACTCGTCCAAGCCATGTTTTTCAATAG

Reverse complement sequence

CTATTGAAAAACATGGCTTGGACGAGTGGTGTAGCAGCATTGGCGACTTCATCTCTAGCTCCTTCAAGCCTCTTGATTTTGTTGACTAAGACATCGAATT[A/G]
AGCCTGGGATTTGATTTTGCGATCTGTACGAGTAAGACTCACGTAAGCGAGAGGGCATGAAGATAAGAGTGGTTTTTGGAATTCTAGCTACAAGTACCTT

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	32.00%	11.60%	1.02%	55.33%	NA
All Indica	2759	32.70%	2.50%	1.05%	63.72%	NA
All Japonica	1512	31.10%	26.40%	0.86%	41.67%	NA
Aus	269	32.70%	21.20%	1.12%	44.98%	NA
Indica I	595	14.10%	4.40%	1.34%	80.17%	NA
Indica II	465	16.30%	1.30%	1.29%	81.08%	NA
Indica III	913	56.10%	0.70%	0.44%	42.83%	NA
Indica Intermediate	786	29.40%	3.90%	1.40%	65.27%	NA
Temperate Japonica	767	19.30%	20.50%	1.56%	58.67%	NA
Tropical Japonica	504	50.20%	32.50%	0.20%	17.06%	NA
Japonica Intermediate	241	28.60%	32.40%	0.00%	39.00%	NA
VI/Aromatic	96	22.90%	5.20%	2.08%	69.79%	NA
Intermediate	90	33.30%	22.20%	1.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127863155	T -> DEL	N	N	silent_mutation	Average:21.564; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg1127863155	T -> C	LOC_Os11g46020.1	upstream_gene_variant ; 4215.0bp to feature; MODIFIER	silent_mutation	Average:21.564; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg1127863155	T -> C	LOC_Os11g46040.1	downstream_gene_variant ; 1392.0bp to feature; MODIFIER	silent_mutation	Average:21.564; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg1127863155	T -> C	LOC_Os11g46030.1	intron_variant ; MODIFIER	silent_mutation	Average:21.564; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127863155	3.43E-06	3.43E-06	mr1048	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