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Detailed information for vg0708274941:

Variant ID: vg0708274941 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8274941
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGGAGCGGATTGATGAACCCTAGTTTTGCCGGCGCAGTTTTGTACTATAGCAGAGAATGGGGAAAATGGCGAGAGTCTCGGCGGGGAAGACGAAGAGA[C/T]
GTTTTATTTTGGTATTATTAGGGTATCGGGAGTACTAATGGGCTTGGGCCTAAACATAGTACTTCAGCCCAATTTTATTTTCAGCGTGGCCCGTTGTGAT

Reverse complement sequence

ATCACAACGGGCCACGCTGAAAATAAAATTGGGCTGAAGTACTATGTTTAGGCCCAAGCCCATTAGTACTCCCGATACCCTAATAATACCAAAATAAAAC[G/A]
TCTCTTCGTCTTCCCCGCCGAGACTCTCGCCATTTTCCCCATTCTCTGCTATAGTACAAAACTGCGCCGGCAAAACTAGGGTTCATCAATCCGCTCCAAT

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	85.70%	0.60%	9.18%	4.49%	NA
All Indica	2759	83.00%	1.00%	11.78%	4.17%	NA
All Japonica	1512	86.80%	0.10%	6.94%	6.15%	NA
Aus	269	98.50%	0.00%	0.37%	1.12%	NA
Indica I	595	76.60%	1.00%	18.66%	3.70%	NA
Indica II	465	88.60%	0.20%	7.31%	3.87%	NA
Indica III	913	88.90%	1.20%	4.93%	4.93%	NA
Indica Intermediate	786	77.70%	1.30%	17.18%	3.82%	NA
Temperate Japonica	767	75.40%	0.00%	12.91%	11.73%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	97.10%	0.00%	1.66%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0708274941	C -> DEL	N	N	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.1	upstream_gene_variant ; 723.0bp to feature; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.5	upstream_gene_variant ; 3833.0bp to feature; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.3	upstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.2	intron_variant ; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.4	intron_variant ; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0708274941	C -> T	LOC_Os07g14514.6	intron_variant ; MODIFIER	silent_mutation	Average:43.436; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708274941	4.98E-06	4.98E-06	mr1392	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