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Detailed information for vg0713864611:

Variant ID: vg0713864611 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13864611
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGTTTAAAACCTTCTTTTGACTAAAATTCTTTTATTCAAATTTAGTTTGAAAACCCCTTTCTATTTTCATGAATTATGGTCCAAGAAATTCTCCACTA[C/T]
TGTCCTAGAACCTAAACCAAACGATTCCAATTTTATTGGAATTAATTGTCGACCCATCCTTTGATTTTAAACCTATCCTTTGATTCCAAACCTATTCTTA

Reverse complement sequence

TAAGAATAGGTTTGGAATCAAAGGATAGGTTTAAAATCAAAGGATGGGTCGACAATTAATTCCAATAAAATTGGAATCGTTTGGTTTAGGTTCTAGGACA[G/A]
TAGTGGAGAATTTCTTGGACCATAATTCATGAAAATAGAAAGGGGTTTTCAAACTAAATTTGAATAAAAGAATTTTAGTCAAAAGAAGGTTTTAAACCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.10%	6.90%	6.50%	13.46%	NA
All Indica	2759	85.80%	0.90%	4.46%	8.77%	NA
All Japonica	1512	46.80%	19.20%	8.80%	25.20%	NA
Aus	269	84.40%	0.00%	13.38%	2.23%	NA
Indica I	595	70.60%	0.80%	7.23%	21.34%	NA
Indica II	465	94.00%	1.70%	1.29%	3.01%	NA
Indica III	913	98.20%	0.00%	0.33%	1.42%	NA
Indica Intermediate	786	78.10%	1.70%	9.03%	11.20%	NA
Temperate Japonica	767	28.40%	27.00%	14.47%	30.12%	NA
Tropical Japonica	504	84.10%	8.30%	0.79%	6.75%	NA
Japonica Intermediate	241	27.40%	17.00%	7.47%	48.13%	NA
VI/Aromatic	96	92.70%	0.00%	2.08%	5.21%	NA
Intermediate	90	72.20%	11.10%	14.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713864611	C -> DEL	N	N	silent_mutation	Average:17.759; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0713864611	C -> T	LOC_Os07g24370.1	downstream_gene_variant ; 4944.0bp to feature; MODIFIER	silent_mutation	Average:17.759; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0713864611	C -> T	LOC_Os07g24350-LOC_Os07g24370	intergenic_region ; MODIFIER	silent_mutation	Average:17.759; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713864611	3.15E-07	3.15E-07	mr1955	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