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Detailed information for vg1004234880:

Variant ID: vg1004234880 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4234880
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACATGTTTTGGATTTGGATTCGGGCCTCCTGACAGCATCAACTTCAAACGGACCTAGCCGCTGATCTAGAAGGAATTTCGGGGCCCGTGAGTACTTCTT[G/C]
GAAAGCTTAGGGAGTCTAATTTCAGATGGTTTTGGTCCCACATCAAAATTCCTACCGAGCTACTGGGAATCTGCAAAACAAGCCACATATCTCATCCAGT

Reverse complement sequence

ACTGGATGAGATATGTGGCTTGTTTTGCAGATTCCCAGTAGCTCGGTAGGAATTTTGATGTGGGACCAAAACCATCTGAAATTAGACTCCCTAAGCTTTC[C/G]
AAGAAGTACTCACGGGCCCCGAAATTCCTTCTAGATCAGCGGCTAGGTCCGTTTGAAGTTGATGCTGTCAGGAGGCCCGAATCCAAATCCAAAACATGTA

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	98.30%	1.20%	0.49%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.80%	3.70%	1.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	89.80%	7.30%	2.87%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg1004234880	G -> C	LOC_Os10g07622.1	upstream_gene_variant ; 813.0bp to feature; MODIFIER	silent_mutation	Average:29.714; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg1004234880	G -> C	LOC_Os10g07626.1	upstream_gene_variant ; 2310.0bp to feature; MODIFIER	silent_mutation	Average:29.714; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg1004234880	G -> C	LOC_Os10g07618.1	downstream_gene_variant ; 3185.0bp to feature; MODIFIER	silent_mutation	Average:29.714; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg1004234880	G -> C	LOC_Os10g07624.1	downstream_gene_variant ; 630.0bp to feature; MODIFIER	silent_mutation	Average:29.714; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg1004234880	G -> C	LOC_Os10g07622-LOC_Os10g07624	intergenic_region ; MODIFIER	silent_mutation	Average:29.714; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004234880	1.61E-06	1.61E-06	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