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Detailed information for vg1007489797:

Variant ID: vg1007489797 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 7489797
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCGGTCTGACCGCCGGTGTCTCACCGGTTAGACCGCCGAACCCGAGCAAACACAACTCGAAGAACTCTAGATGTAGATGACAACTTTATTACTTCTCT[C/A]
TGTGTTTACAAAGTGCAACAACAGCACTCCTCATGAAAATTTCGACTAAACTCGAAACCCTAACTCAACTATTAATTCAATGCTCTCATAAGAGATACCG

Reverse complement sequence

CGGTATCTCTTATGAGAGCATTGAATTAATAGTTGAGTTAGGGTTTCGAGTTTAGTCGAAATTTTCATGAGGAGTGCTGTTGTTGCACTTTGTAAACACA[G/T]
AGAGAAGTAATAAAGTTGTCATCTACATCTAGAGTTCTTCGAGTTGTGTTTGCTCGGGTTCGGCGGTCTAACCGGTGAGACACCGGCGGTCAGACCGGCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	3.30%	5.82%	25.20%	NA
All Indica	2759	68.90%	2.60%	6.92%	21.60%	NA
All Japonica	1512	52.50%	5.20%	5.29%	36.97%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	30.80%	0.50%	13.45%	55.29%	NA
Indica II	465	82.80%	1.10%	4.09%	12.04%	NA
Indica III	913	84.20%	5.00%	3.61%	7.12%	NA
Indica Intermediate	786	71.80%	2.20%	7.51%	18.58%	NA
Temperate Japonica	767	59.30%	0.00%	1.17%	39.50%	NA
Tropical Japonica	504	36.90%	14.30%	11.90%	36.90%	NA
Japonica Intermediate	241	63.50%	2.90%	4.56%	29.05%	NA
VI/Aromatic	96	78.10%	1.00%	3.12%	17.71%	NA
Intermediate	90	74.40%	4.40%	1.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1007489797	C -> A	LOC_Os10g13770.1	upstream_gene_variant ; 409.0bp to feature; MODIFIER	silent_mutation	Average:16.893; most accessible tissue: Callus, score: 44.827	N	N	N	N
vg1007489797	C -> A	LOC_Os10g13780.1	upstream_gene_variant ; 1752.0bp to feature; MODIFIER	silent_mutation	Average:16.893; most accessible tissue: Callus, score: 44.827	N	N	N	N
vg1007489797	C -> A	LOC_Os10g13790.1	downstream_gene_variant ; 2999.0bp to feature; MODIFIER	silent_mutation	Average:16.893; most accessible tissue: Callus, score: 44.827	N	N	N	N
vg1007489797	C -> A	LOC_Os10g13770-LOC_Os10g13780	intergenic_region ; MODIFIER	silent_mutation	Average:16.893; most accessible tissue: Callus, score: 44.827	N	N	N	N
vg1007489797	C -> DEL	N	N	silent_mutation	Average:16.893; most accessible tissue: Callus, score: 44.827	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1007489797	NA	9.66E-07	mr1134	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
vg1007489797	NA	1.53E-06	mr1135	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
vg1007489797	NA	1.65E-06	mr1504	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
vg1007489797	9.41E-07	1.94E-08	mr1134_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