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Detailed information for vg1020448314:

Variant ID: vg1020448314 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20448314
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGGCACACTCTGGCAACGGTAAGGCGAAGGGATGGGAAGGGAGGCTGCGCGGCGGTGCGCCGCCCGTGAGGACGACGCGGGGGCCCTCGGGTCCTCTT[C/A]
GTTTCGCACTACCCAGAGAAGAATTACATGAACAAAGTAGTATGACATAGTTGTTCTTTTAGATAATAAAAATGGTTTACATACCCGGCTTCTACCCTAA

Reverse complement sequence

TTAGGGTAGAAGCCGGGTATGTAAACCATTTTTATTATCTAAAAGAACAACTATGTCATACTACTTTGTTCATGTAATTCTTCTCTGGGTAGTGCGAAAC[G/T]
AAGAGGACCCGAGGGCCCCCGCGTCGTCCTCACGGGCGGCGCACCGCCGCGCAGCCTCCCTTCCCATCCCTTCGCCTTACCGTTGCCAGAGTGTGCCACC

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	32.60%	3.10%	0.23%	64.11%	NA
All Indica	2759	5.10%	0.10%	0.25%	94.56%	NA
All Japonica	1512	81.90%	9.40%	0.26%	8.40%	NA
Aus	269	42.80%	0.00%	0.00%	57.25%	NA
Indica I	595	10.90%	0.20%	0.34%	88.57%	NA
Indica II	465	3.70%	0.20%	0.43%	95.70%	NA
Indica III	913	1.10%	0.00%	0.00%	98.90%	NA
Indica Intermediate	786	6.20%	0.00%	0.38%	93.38%	NA
Temperate Japonica	767	96.90%	0.90%	0.00%	2.22%	NA
Tropical Japonica	504	56.00%	24.40%	0.60%	19.05%	NA
Japonica Intermediate	241	88.80%	5.00%	0.41%	5.81%	NA
VI/Aromatic	96	8.30%	0.00%	0.00%	91.67%	NA
Intermediate	90	40.00%	2.20%	0.00%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020448314	C -> A	LOC_Os10g38170.1	upstream_gene_variant ; 2555.0bp to feature; MODIFIER	silent_mutation	Average:13.263; most accessible tissue: Callus, score: 89.632	N	N	N	N
vg1020448314	C -> A	LOC_Os10g38189.1	downstream_gene_variant ; 778.0bp to feature; MODIFIER	silent_mutation	Average:13.263; most accessible tissue: Callus, score: 89.632	N	N	N	N
vg1020448314	C -> A	LOC_Os10g38170-LOC_Os10g38189	intergenic_region ; MODIFIER	silent_mutation	Average:13.263; most accessible tissue: Callus, score: 89.632	N	N	N	N
vg1020448314	C -> DEL	N	N	silent_mutation	Average:13.263; most accessible tissue: Callus, score: 89.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020448314	NA	1.49E-06	mr1243_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
vg1020448314	4.27E-06	4.27E-06	mr1603_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