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Detailed information for vg0210111974:

Variant ID: vg0210111974 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10111974
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCAGCGAGAACTCATCAGGGTGCGTCGGGATGGTAGTCGCGATACCGCACTCCCCGGCAAGTTGGTGCAGGCTGGTGAACGATGTTCGCAACGAATCG[T/C]
GGATGTCGAGTATGTTGCCCTCGAGCTCCGACATCCGGTGCTCGAGCCCGCGTCGCTACCTCTCGTTGCCAGCTACCAGCTCCCTCATCTTCAGGAGGTC

Reverse complement sequence

GACCTCCTGAAGATGAGGGAGCTGGTAGCTGGCAACGAGAGGTAGCGACGCGGGCTCGAGCACCGGATGTCGGAGCTCGAGGGCAACATACTCGACATCC[A/G]
CGATTCGTTGCGAACATCGTTCACCAGCCTGCACCAACTTGCCGGGGAGTGCGGTATCGCGACTACCATCCCGACGCACCCTGATGAGTTCTCGCTGACA

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	51.20%	30.90%	0.99%	16.89%	NA
All Indica	2759	32.00%	38.30%	1.49%	28.20%	NA
All Japonica	1512	86.10%	13.20%	0.20%	0.46%	NA
Aus	269	37.20%	61.70%	1.12%	0.00%	NA
Indica I	595	36.30%	22.20%	1.51%	40.00%	NA
Indica II	465	29.90%	30.80%	2.37%	36.99%	NA
Indica III	913	32.20%	56.30%	0.44%	11.06%	NA
Indica Intermediate	786	29.60%	34.20%	2.16%	33.97%	NA
Temperate Japonica	767	76.10%	22.80%	0.39%	0.65%	NA
Tropical Japonica	504	97.00%	2.80%	0.00%	0.20%	NA
Japonica Intermediate	241	95.00%	4.60%	0.00%	0.41%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	55.60%	30.00%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210111974	T -> DEL	N	N	silent_mutation	Average:40.353; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N
vg0210111974	T -> C	LOC_Os02g17570.1	downstream_gene_variant ; 2042.0bp to feature; MODIFIER	silent_mutation	Average:40.353; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N
vg0210111974	T -> C	LOC_Os02g17580.1	intron_variant ; MODIFIER	silent_mutation	Average:40.353; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210111974	4.29E-06	4.29E-06	mr1360	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