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Detailed information for vg1000709547:

Variant ID: vg1000709547 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 709547
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGATCTTATCTGATTTAACTAATTTATATCTTATATGCTTGATTGGCATGTTAAATCCGCCCTTTATGTTAAGATCTTGTTGTGTTTAGGTATATTAA[C/G]
CTTTTTGTTTGATATATCCTACTTGCTTTAATATCTTAATATAGAGTGGTATTGGAGTAATTAGCCGATACATGCTAGATCTATCTGATCGGCTATGCTA

Reverse complement sequence

TAGCATAGCCGATCAGATAGATCTAGCATGTATCGGCTAATTACTCCAATACCACTCTATATTAAGATATTAAAGCAAGTAGGATATATCAAACAAAAAG[G/C]
TTAATATACCTAAACACAACAAGATCTTAACATAAAGGGCGGATTTAACATGCCAATCAAGCATATAAGATATAAATTAGTTAAATCAGATAAGATCGGC

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	83.50%	16.50%	0.00%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	51.00%	49.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	21.10%	78.90%	0.00%	0.00%	NA
Tropical Japonica	504	94.40%	5.60%	0.00%	0.00%	NA
Japonica Intermediate	241	55.20%	44.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg1000709547	C -> G	LOC_Os10g02120.1	upstream_gene_variant ; 4320.0bp to feature; MODIFIER	silent_mutation	Average:41.025; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1000709547	C -> G	LOC_Os10g02120-LOC_Os10g02130	intergenic_region ; MODIFIER	silent_mutation	Average:41.025; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000709547	1.36E-25	1.87E-47	mr1300	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
vg1000709547	4.44E-12	6.18E-17	mr1300	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
vg1000709547	1.97E-29	7.02E-70	mr1310	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
vg1000709547	1.86E-13	1.32E-20	mr1310	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
vg1000709547	1.66E-06	NA	mr1498	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
vg1000709547	4.33E-39	5.44E-86	mr1926	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
vg1000709547	2.18E-15	1.62E-24	mr1926	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
vg1000709547	1.04E-15	1.67E-21	mr1959	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
vg1000709547	1.08E-09	5.37E-12	mr1959	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
vg1000709547	3.56E-45	4.77E-81	mr1310_2	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
vg1000709547	4.36E-23	6.21E-35	mr1310_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
vg1000709547	6.36E-06	6.36E-06	mr1581_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
vg1000709547	1.22E-23	4.15E-34	mr1959_2	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
vg1000709547	3.44E-14	4.64E-21	mr1959_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