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Detailed information for vg0711675998:

Variant ID: vg0711675998 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11675998
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGCACACGAAAGAGTGCGAGAGCTTAGAAGATCACACGCAGCGCCCCCTACCTGGCGCGCCAGATGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCG[T/C]
AGGCCCCCCTTTGCCGGTTCGGCCGGGGACCCTGGGTGAGATTCTAAGCTCCTTATCTGTGGAAGATTCGCGAGAGTGGAAAAAACACAAGACACGGGCG

Reverse complement sequence

CGCCCGTGTCTTGTGTTTTTTCCACTCTCGCGAATCTTCCACAGATAAGGAGCTTAGAATCTCACCCAGGGTCCCCGGCCGAACCGGCAAAGGGGGGCCT[A/G]
CGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCATCTGGCGCGCCAGGTAGGGGGCGCTGCGTGTGATCTTCTAAGCTCTCGCACTCTTTCGTGTGCGC

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	37.40%	10.50%	17.69%	34.41%	NA
All Indica	2759	32.50%	2.40%	22.65%	42.44%	NA
All Japonica	1512	51.60%	26.60%	2.51%	19.31%	NA
Aus	269	13.80%	2.60%	46.47%	37.17%	NA
Indica I	595	12.80%	1.30%	21.68%	64.20%	NA
Indica II	465	33.80%	5.80%	25.59%	34.84%	NA
Indica III	913	49.60%	1.40%	20.59%	28.37%	NA
Indica Intermediate	786	26.80%	2.30%	24.05%	46.82%	NA
Temperate Japonica	767	26.70%	38.60%	3.13%	31.55%	NA
Tropical Japonica	504	84.50%	11.50%	0.99%	2.98%	NA
Japonica Intermediate	241	61.80%	19.90%	3.73%	14.52%	NA
VI/Aromatic	96	20.80%	4.20%	35.42%	39.58%	NA
Intermediate	90	37.80%	18.90%	15.56%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711675998	T -> DEL	N	N	silent_mutation	Average:19.496; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0711675998	T -> C	LOC_Os07g20250.1	upstream_gene_variant ; 123.0bp to feature; MODIFIER	silent_mutation	Average:19.496; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0711675998	T -> C	LOC_Os07g20240.1	downstream_gene_variant ; 2169.0bp to feature; MODIFIER	silent_mutation	Average:19.496; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0711675998	T -> C	LOC_Os07g20260.1	downstream_gene_variant ; 2726.0bp to feature; MODIFIER	silent_mutation	Average:19.496; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0711675998	T -> C	LOC_Os07g20250-LOC_Os07g20260	intergenic_region ; MODIFIER	silent_mutation	Average:19.496; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711675998	1.45E-06	1.46E-06	mr1894	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