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Detailed information for vg1000968214:

Variant ID: vg1000968214 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 968214
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCTGTCACAGATGGTTGATTGACAACTTTCATAACTGCCAAGTTTAGCCAGGTTTGCAGCAACCACCATGGTCCACCTGCCCCAACTACTGAGCCGAC[G/A]
GCTATCTTGGCCGATGCATTGTTCAACATTTGATATAGATAGCCGAGGAGGATTTTGCCCAAGGGAAATTGTCAATCGTGATTCTAGGGCTTCGGCTACA

Reverse complement sequence

TGTAGCCGAAGCCCTAGAATCACGATTGACAATTTCCCTTGGGCAAAATCCTCCTCGGCTATCTATATCAAATGTTGAACAATGCATCGGCCAAGATAGC[C/T]
GTCGGCTCAGTAGTTGGGGCAGGTGGACCATGGTGGTTGCTGCAAACCTGGCTAAACTTGGCAGTTATGAAAGTTGTCAATCAACCATCTGTGACAGAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	37.00%	5.44%	7.55%	NA
All Indica	2759	28.50%	60.40%	7.47%	3.59%	NA
All Japonica	1512	91.30%	3.30%	1.19%	4.17%	NA
Aus	269	13.00%	7.40%	8.92%	70.63%	NA
Indica I	595	57.80%	20.30%	15.13%	6.72%	NA
Indica II	465	8.20%	86.70%	3.44%	1.72%	NA
Indica III	913	20.20%	74.40%	3.94%	1.53%	NA
Indica Intermediate	786	28.10%	59.00%	8.14%	4.71%	NA
Temperate Japonica	767	98.40%	0.70%	0.13%	0.78%	NA
Tropical Japonica	504	84.30%	7.90%	2.58%	5.16%	NA
Japonica Intermediate	241	83.40%	2.10%	1.66%	12.86%	NA
VI/Aromatic	96	91.70%	2.10%	4.17%	2.08%	NA
Intermediate	90	78.90%	12.20%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000968214	G -> A	LOC_Os10g02544.1	downstream_gene_variant ; 2699.0bp to feature; MODIFIER	silent_mutation	Average:16.844; most accessible tissue: Callus, score: 40.304	N	N	N	N
vg1000968214	G -> A	LOC_Os10g02570.1	downstream_gene_variant ; 2644.0bp to feature; MODIFIER	silent_mutation	Average:16.844; most accessible tissue: Callus, score: 40.304	N	N	N	N
vg1000968214	G -> A	LOC_Os10g02560.1	intron_variant ; MODIFIER	silent_mutation	Average:16.844; most accessible tissue: Callus, score: 40.304	N	N	N	N
vg1000968214	G -> DEL	N	N	silent_mutation	Average:16.844; most accessible tissue: Callus, score: 40.304	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000968214	7.88E-06	NA	mr1212	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
vg1000968214	1.53E-06	2.93E-06	mr1212	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
vg1000968214	9.61E-06	NA	mr1542	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