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Detailed information for vg0712338155:

Variant ID: vg0712338155 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12338155
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCAGGAGTTCTACCTCTTTATTCTCAGCCTTCTGCAAGTAAATCTAGCTCTACACAGATATTACCTCTCATGCATTCATTGTTGAATAATATAATAGC[T/A]
TGCTGAGTACGTTGTACTCACCCTTGCTTCAACCCCTCTTTTTCAGAGTTTAATTGGAGTTTTTGCCGAAGCTGGGAGTTCAATCACATAAGTTAGTTCC

Reverse complement sequence

GGAACTAACTTATGTGATTGAACTCCCAGCTTCGGCAAAAACTCCAATTAAACTCTGAAAAAGAGGGGTTGAAGCAAGGGTGAGTACAACGTACTCAGCA[A/T]
GCTATTATATTATTCAACAATGAATGCATGAGAGGTAATATCTGTGTAGAGCTAGATTTACTTGCAGAAGGCTGAGAATAAAGAGGTAGAACTCCTGAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.80%	7.90%	1.44%	5.84%	NA
All Indica	2759	98.80%	0.00%	0.62%	0.58%	NA
All Japonica	1512	58.20%	24.10%	2.71%	15.01%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	95.80%	0.10%	2.16%	1.91%	NA
Temperate Japonica	767	68.40%	2.20%	3.91%	25.42%	NA
Tropical Japonica	504	31.70%	66.50%	1.59%	0.20%	NA
Japonica Intermediate	241	80.90%	5.00%	1.24%	12.86%	NA
VI/Aromatic	96	58.30%	0.00%	8.33%	33.33%	NA
Intermediate	90	90.00%	8.90%	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
vg0712338155	T -> DEL	N	N	silent_mutation	Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0712338155	T -> A	LOC_Os07g22080.1	upstream_gene_variant ; 4153.0bp to feature; MODIFIER	silent_mutation	Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0712338155	T -> A	LOC_Os07g22060.1	downstream_gene_variant ; 3593.0bp to feature; MODIFIER	silent_mutation	Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0712338155	T -> A	LOC_Os07g22070.1	intron_variant ; MODIFIER	silent_mutation	Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712338155	NA	2.03E-06	mr1194_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
vg0712338155	NA	3.13E-07	mr1363_2	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
vg0712338155	NA	8.85E-06	mr1786_2	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
vg0712338155	1.00E-07	NA	mr1850_2	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