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Detailed information for vg0922386993:

Variant ID: vg0922386993 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22386993
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTCCTTCACAATTTTGTAACGTAGAAGATAGGATTACTAATCCATTGCAGATCCCAAAATGTTGAACGTGCTAGTTTTATTGTACTTTTATATCTT[C/G]
ATGAATGTGCATGATGATTTGCTTGATACTACTTTGATTAAACACATACTTCCTCTGTCCCCCAAAAAAAATAACCTAGGAGGGGATGTGACATTTTCTA

Reverse complement sequence

TAGAAAATGTCACATCCCCTCCTAGGTTATTTTTTTTGGGGGACAGAGGAAGTATGTGTTTAATCAAAGTAGTATCAAGCAAATCATCATGCACATTCAT[G/C]
AAGATATAAAAGTACAATAAAACTAGCACGTTCAACATTTTGGGATCTGCAATGGATTAGTAATCCTATCTTCTACGTTACAAAATTGTGAAGGAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.40%	0.30%	0.23%	0.00%	NA
All Indica	2759	99.20%	0.40%	0.40%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	98.00%	1.00%	1.01%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	98.90%	0.60%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0922386993	C -> G	LOC_Os09g38980.1	3_prime_UTR_variant ; 360.0bp to feature; MODIFIER	N	Average:68.259; most accessible tissue: Callus, score: 92.72	N	N	N	N
vg0922386993	C -> G	LOC_Os09g38980.2	3_prime_UTR_variant ; 360.0bp to feature; MODIFIER	N	Average:68.259; most accessible tissue: Callus, score: 92.72	N	N	N	N
vg0922386993	C -> G	LOC_Os09g38990.1	upstream_gene_variant ; 761.0bp to feature; MODIFIER	N	Average:68.259; most accessible tissue: Callus, score: 92.72	N	N	N	N
vg0922386993	C -> G	LOC_Os09g39000.1	upstream_gene_variant ; 4317.0bp to feature; MODIFIER	N	Average:68.259; most accessible tissue: Callus, score: 92.72	N	N	N	N
vg0922386993	C -> G	LOC_Os09g38970.1	downstream_gene_variant ; 4501.0bp to feature; MODIFIER	N	Average:68.259; most accessible tissue: Callus, score: 92.72	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922386993	9.53E-07	9.53E-07	mr1440_2	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