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Detailed information for vg0221860877:

Variant ID: vg0221860877 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21860877
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAACAATATCGATGTACGTTTATTGATCTAATCCCTTATGAAAGGTGTTGTCTTGAAATTGTTGTGGTGAAAACCTAACTTTTTGATAGGACAATATG[G/C]
TAAACATATATATATGATATTTTCTTTAGGAAGGTACTATCGCAGTCTCTTGGAGAGTGCCTCGTTTGCATAGATGGCCTTCATGTATTCTCTTTTCATC

Reverse complement sequence

GATGAAAAGAGAATACATGAAGGCCATCTATGCAAACGAGGCACTCTCCAAGAGACTGCGATAGTACCTTCCTAAAGAAAATATCATATATATATGTTTA[C/G]
CATATTGTCCTATCAAAAAGTTAGGTTTTCACCACAACAATTTCAAGACAACACCTTTCATAAGGGATTAGATCAATAAACGTACATCGATATTGTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.50%	4.80%	0.68%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	83.10%	14.80%	2.05%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	92.60%	5.20%	2.22%	0.00%	NA
Tropical Japonica	504	71.00%	27.00%	1.98%	0.00%	NA
Japonica Intermediate	241	78.40%	19.90%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221860877	G -> C	LOC_Os02g36220.1	intron_variant ; MODIFIER	silent_mutation	Average:43.026; most accessible tissue: Zhenshan97 young leaf, score: 53.969	N	N	N	N
vg0221860877	G -> C	LOC_Os02g36220.2	intron_variant ; MODIFIER	silent_mutation	Average:43.026; most accessible tissue: Zhenshan97 young leaf, score: 53.969	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221860877	NA	7.37E-06	mr1502	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
vg0221860877	NA	4.28E-09	mr1543	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
vg0221860877	6.91E-11	4.22E-16	mr1871	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
vg0221860877	3.40E-12	1.27E-15	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
vg0221860877	9.73E-06	2.13E-08	mr1502_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
vg0221860877	5.53E-07	7.57E-11	mr1543_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
vg0221860877	5.45E-06	1.15E-07	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
vg0221860877	4.11E-10	8.77E-15	mr1742_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
vg0221860877	1.08E-18	4.38E-23	mr1871_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