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Detailed information for vg0221010130:

Variant ID: vg0221010130 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21010130
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGAACACCGCATACAGATCTAGTCCATAAGTACGTACTCCTATAGTATGGCCCTGTTTAGTACCAAAGTTTTTTTTCAAACTTCCAACTTTTCAATTT[C/T]
CATCACATCAAATTTTTCATACACACATAACTTTGCTATCACATCATACCAATTTCAACCAAACTTTCAAACTTCAGTGTGAACTTAACACAGCCTATAC

Reverse complement sequence

GTATAGGCTGTGTTAAGTTCACACTGAAGTTTGAAAGTTTGGTTGAAATTGGTATGATGTGATAGCAAAGTTATGTGTGTATGAAAAATTTGATGTGATG[G/A]
AAATTGAAAAGTTGGAAGTTTGAAAAAAAACTTTGGTACTAAACAGGGCCATACTATAGGAGTACGTACTTATGGACTAGATCTGTATGCGGTGTTCTAG

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	58.90%	0.60%	2.31%	38.28%	NA
All Indica	2759	40.50%	0.00%	2.03%	57.45%	NA
All Japonica	1512	95.60%	1.50%	1.65%	1.26%	NA
Aus	269	24.20%	0.00%	8.92%	66.91%	NA
Indica I	595	23.50%	0.00%	3.19%	73.28%	NA
Indica II	465	37.60%	0.00%	2.80%	59.57%	NA
Indica III	913	58.70%	0.00%	0.88%	40.42%	NA
Indica Intermediate	786	33.80%	0.10%	2.04%	63.99%	NA
Temperate Japonica	767	96.00%	0.00%	3.00%	1.04%	NA
Tropical Japonica	504	95.20%	4.00%	0.40%	0.40%	NA
Japonica Intermediate	241	95.40%	0.80%	0.00%	3.73%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	67.80%	3.30%	3.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221010130	C -> T	LOC_Os02g35010.1	upstream_gene_variant ; 1721.0bp to feature; MODIFIER	silent_mutation	Average:51.987; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg0221010130	C -> T	LOC_Os02g35020.1	downstream_gene_variant ; 4317.0bp to feature; MODIFIER	silent_mutation	Average:51.987; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg0221010130	C -> T	LOC_Os02g35010-LOC_Os02g35020	intergenic_region ; MODIFIER	silent_mutation	Average:51.987; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg0221010130	C -> DEL	N	N	silent_mutation	Average:51.987; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221010130	9.10E-06	NA	mr1101	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
vg0221010130	2.59E-06	NA	mr1150	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