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Detailed information for vg1012832874:

Variant ID: vg1012832874 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12832874
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCCTACCTCATGTATAAATAGACAGGGAGTGTGAGGCTTCCCGGTATCGCTTTCGAGAGCAATTGAGTTGATAGTTGAGTTAGGGTTTCGAGCTTACT[C/T]
GAGTTTTTTGTTTGGAGTGATGTTGGTGCACTTTGTAAACACAGAGAGAATCAATAAAGTCGTCATCCACTTTAAGAGTTATTCAATTTGTGTTTCATCG

Reverse complement sequence

CGATGAAACACAAATTGAATAACTCTTAAAGTGGATGACGACTTTATTGATTCTCTCTGTGTTTACAAAGTGCACCAACATCACTCCAAACAAAAAACTC[G/A]
AGTAAGCTCGAAACCCTAACTCAACTATCAACTCAATTGCTCTCGAAAGCGATACCGGGAAGCCTCACACTCCCTGTCTATTTATACATGAGGTAGGCAG

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	57.70%	1.20%	2.71%	38.40%	NA
All Indica	2759	37.80%	0.00%	2.03%	60.17%	NA
All Japonica	1512	82.80%	3.60%	4.76%	8.80%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	29.40%	0.00%	2.02%	68.57%	NA
Indica II	465	43.70%	0.00%	2.58%	53.76%	NA
Indica III	913	32.10%	0.00%	1.97%	65.94%	NA
Indica Intermediate	786	47.30%	0.00%	1.78%	50.89%	NA
Temperate Japonica	767	82.40%	6.90%	8.34%	2.35%	NA
Tropical Japonica	504	83.50%	0.00%	0.40%	16.07%	NA
Japonica Intermediate	241	82.60%	0.80%	2.49%	14.11%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	77.80%	1.10%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012832874	C -> T	LOC_Os10g24920.1	upstream_gene_variant ; 510.0bp to feature; MODIFIER	silent_mutation	Average:13.08; most accessible tissue: Callus, score: 30.17	N	N	N	N
vg1012832874	C -> T	LOC_Os10g24940.1	upstream_gene_variant ; 3105.0bp to feature; MODIFIER	silent_mutation	Average:13.08; most accessible tissue: Callus, score: 30.17	N	N	N	N
vg1012832874	C -> T	LOC_Os10g24920-LOC_Os10g24940	intergenic_region ; MODIFIER	silent_mutation	Average:13.08; most accessible tissue: Callus, score: 30.17	N	N	N	N
vg1012832874	C -> DEL	N	N	silent_mutation	Average:13.08; most accessible tissue: Callus, score: 30.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012832874	NA	6.21E-09	mr1354	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
vg1012832874	NA	9.09E-06	mr1038_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
vg1012832874	9.71E-06	9.30E-10	mr1354_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
vg1012832874	3.23E-08	3.23E-08	mr1499_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
vg1012832874	NA	1.15E-06	mr1829_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
vg1012832874	NA	5.43E-08	mr1902_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