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Detailed information for vg0412100387:

Variant ID: vg0412100387 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12100387
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTGAGAACAATTCTCAGGTTGCGATACCAATCCATGAAGTTTGTTCCAGTCAACTTCTCTTTCTCAAGAATAGACCGCAAGTTAAAATTGGATGGTGCA[T/G]
GAGCTGCCATAATCTACAATAGAAATATATGTATGCAAAATCAGCACCATGTTTACATTTAACCTTTCATCAAACAATTTAACAAAAGATACTCCCATTA

Reverse complement sequence

TAATGGGAGTATCTTTTGTTAAATTGTTTGATGAAAGGTTAAATGTAAACATGGTGCTGATTTTGCATACATATATTTCTATTGTAGATTATGGCAGCTC[A/C]
TGCACCATCCAATTTTAACTTGCGGTCTATTCTTGAGAAAGAGAAGTTGACTGGAACAAACTTCATGGATTGGTATCGCAACCTGAGAATTGTTCTCAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.60%	1.70%	4.13%	57.60%	NA
All Indica	2759	3.30%	2.60%	5.51%	88.58%	NA
All Japonica	1512	98.90%	0.20%	0.20%	0.73%	NA
Aus	269	5.20%	0.00%	11.90%	82.90%	NA
Indica I	595	1.70%	0.00%	1.34%	96.97%	NA
Indica II	465	3.70%	7.10%	16.13%	73.12%	NA
Indica III	913	3.30%	2.70%	3.61%	90.36%	NA
Indica Intermediate	786	4.20%	1.90%	4.58%	89.31%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	96.70%	1.20%	1.24%	0.83%	NA
VI/Aromatic	96	86.50%	0.00%	3.12%	10.42%	NA
Intermediate	90	54.40%	2.20%	5.56%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412100387	T -> DEL	LOC_Os04g21410.1	N	frameshift_variant	Average:7.66; most accessible tissue: Callus, score: 24.523	N	N	N	N
vg0412100387	T -> G	LOC_Os04g21410.1	missense_variant ; p.His81Pro; MODERATE	nonsynonymous_codon ; H81P	Average:7.66; most accessible tissue: Callus, score: 24.523	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412100387	2.86E-07	4.97E-10	mr1071	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
vg0412100387	NA	2.44E-08	mr1080	Ind_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
vg0412100387	1.95E-07	1.42E-09	mr1140	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
vg0412100387	3.78E-08	2.42E-11	mr1203	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
vg0412100387	NA	2.69E-07	mr1395	Ind_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
vg0412100387	NA	3.93E-07	mr1613	Ind_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
vg0412100387	4.42E-07	1.68E-09	mr1618	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
vg0412100387	7.28E-07	1.02E-10	mr1071_2	Ind_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
vg0412100387	9.80E-07	6.45E-11	mr1080_2	Ind_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
vg0412100387	6.34E-07	2.83E-10	mr1203_2	Ind_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
vg0412100387	NA	1.22E-46	mr1458_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
vg0412100387	5.75E-09	1.56E-12	mr1613_2	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
vg0412100387	NA	1.02E-06	mr1619_2	Ind_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
vg0412100387	NA	6.11E-31	mr1913_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