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Detailed information for vg0910260211:

Variant ID: vg0910260211 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10260211
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTGCAATGATTCATATTTGTCACCGTGGGTACCAGCACTATGTCCTGGGACTGGTACTGAGATCGCGGTTTCGTAGGAAGCGGTTCACGCCGTTTTTC[C/G]
TACGACACGCTCCTGTCAGGTGCCATTGTACGGCGGTGCCGGATTGGGGTGTGACAGAAGGGTTCCTCACACTAGAGGAAACTATCCTTTATTAATGAAT

Reverse complement sequence

ATTCATTAATAAAGGATAGTTTCCTCTAGTGTGAGGAACCCTTCTGTCACACCCCAATCCGGCACCGCCGTACAATGGCACCTGACAGGAGCGTGTCGTA[G/C]
GAAAAACGGCGTGAACCGCTTCCTACGAAACCGCGATCTCAGTACCAGTCCCAGGACATAGTGCTGGTACCCACGGTGACAAATATGAATCATTGCAATC

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	82.20%	5.20%	5.73%	6.92%	NA
All Indica	2759	78.10%	1.50%	9.06%	11.38%	NA
All Japonica	1512	88.30%	11.00%	0.53%	0.20%	NA
Aus	269	92.90%	1.10%	4.09%	1.86%	NA
Indica I	595	68.60%	5.50%	15.29%	10.59%	NA
Indica II	465	82.40%	0.40%	4.30%	12.90%	NA
Indica III	913	79.30%	0.20%	7.78%	12.71%	NA
Indica Intermediate	786	81.30%	0.50%	8.65%	9.54%	NA
Temperate Japonica	767	86.30%	12.90%	0.65%	0.13%	NA
Tropical Japonica	504	93.30%	6.20%	0.20%	0.40%	NA
Japonica Intermediate	241	84.20%	14.90%	0.83%	0.00%	NA
VI/Aromatic	96	72.90%	27.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	10.00%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910260211	C -> G	LOC_Os09g16770.1	upstream_gene_variant ; 2639.0bp to feature; MODIFIER	silent_mutation	Average:11.712; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0910260211	C -> G	LOC_Os09g16790.1	upstream_gene_variant ; 3151.0bp to feature; MODIFIER	silent_mutation	Average:11.712; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0910260211	C -> G	LOC_Os09g16780.1	downstream_gene_variant ; 351.0bp to feature; MODIFIER	silent_mutation	Average:11.712; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0910260211	C -> G	LOC_Os09g16770-LOC_Os09g16780	intergenic_region ; MODIFIER	silent_mutation	Average:11.712; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0910260211	C -> DEL	N	N	silent_mutation	Average:11.712; most accessible tissue: Callus, score: 38.711	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910260211	NA	4.47E-07	mr1817_2	Ind_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
vg0910260211	7.59E-07	7.59E-07	mr1912_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