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Detailed information for vg0307993242:

Variant ID: vg0307993242 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7993242
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGCTCCATTGATTTGGGGCCGAGTTTTTCGCGTGCTAATAGTGAAGTACTGCAACGAGAGGGAGAGAGAGATGCAGAGGGGCAAAGGTGTAATTACACT[A/G]
CGTGCTATTGGTGTGGAGATGGCTGTGACCGTGAGCACAACGGTGAATTTCGCATGGGTGCATCAGGGCAATGCACGCTATTCACGCATCAAACCTAGTG

Reverse complement sequence

CACTAGGTTTGATGCGTGAATAGCGTGCATTGCCCTGATGCACCCATGCGAAATTCACCGTTGTGCTCACGGTCACAGCCATCTCCACACCAATAGCACG[T/C]
AGTGTAATTACACCTTTGCCCCTCTGCATCTCTCTCTCCCTCTCGTTGCAGTACTTCACTATTAGCACGCGAAAAACTCGGCCCCAAATCAATGGAGCGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	7.10%	0.42%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	77.20%	21.50%	1.32%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	93.00%	5.70%	1.30%	0.00%	NA
Tropical Japonica	504	73.60%	26.00%	0.40%	0.00%	NA
Japonica Intermediate	241	34.40%	62.20%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg0307993242	A -> G	LOC_Os03g14710.1	upstream_gene_variant ; 4917.0bp to feature; MODIFIER	silent_mutation	Average:68.124; most accessible tissue: Callus, score: 97.897	N	N	N	N
vg0307993242	A -> G	LOC_Os03g14690.1	downstream_gene_variant ; 3805.0bp to feature; MODIFIER	silent_mutation	Average:68.124; most accessible tissue: Callus, score: 97.897	N	N	N	N
vg0307993242	A -> G	LOC_Os03g14700.1	intron_variant ; MODIFIER	silent_mutation	Average:68.124; most accessible tissue: Callus, score: 97.897	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307993242	NA	4.90E-13	mr1871	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
vg0307993242	1.86E-06	NA	mr1238_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
vg0307993242	NA	4.65E-07	mr1308_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
vg0307993242	1.93E-06	NA	mr1484_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
vg0307993242	NA	1.09E-07	mr1554_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
vg0307993242	8.69E-06	1.03E-08	mr1566_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
vg0307993242	NA	5.80E-07	mr1566_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
vg0307993242	NA	2.91E-07	mr1730_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
vg0307993242	NA	1.81E-07	mr1819_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
vg0307993242	NA	7.83E-06	mr1849_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
vg0307993242	NA	5.41E-06	mr1853_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
vg0307993242	NA	2.64E-06	mr1866_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
vg0307993242	NA	6.04E-12	mr1905_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
vg0307993242	NA	1.25E-06	mr1905_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