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Detailed information for vg0429780859:

Variant ID: vg0429780859 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 29780859
Reference Allele: A	Alternative Allele: T,ACTCT,ACACT,ACTCTCTCT
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACCTGCATCGAAGAAAGAGGCAACAAGTCAGAAGACCATAATGCCACAATCCATATTGGCGCGCGCGCGCAGACCCACCCACCCACACACACACACAC[A/T,ACTCT,ACACT,ACTCTCTCT]
CTCTTAAGCTTTGAAAAAAAAGGAAATGAGCTGCAAAAGAACCTGGTATCAAATATTCCATATCGATTTCAGCATCGAGGTGAAAGAAATGAATTGAAAA

Reverse complement sequence

TTTTCAATTCATTTCTTTCACCTCGATGCTGAAATCGATATGGAATATTTGATACCAGGTTCTTTTGCAGCTCATTTCCTTTTTTTTCAAAGCTTAAGAG[T/A,AGAGT,AGTGT,AGAGAGAGT]
GTGTGTGTGTGTGTGGGTGGGTGGGTCTGCGCGCGCGCGCCAATATGGATTGTGGCATTATGGTCTTCTGACTTGTTGCCTCTTTCTTCGATGCAGGTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.50%	2.30%	12.74%	15.38%	ACACT: 1.69%; ACTCT: 1.40%; ACTCTCTCT: 0.04%
All Indica	2759	44.40%	3.90%	21.28%	25.26%	ACACT: 2.86%; ACTCT: 2.36%
All Japonica	1512	99.80%	0.00%	0.07%	0.13%	NA
Aus	269	91.10%	0.40%	1.12%	7.43%	NA
Indica I	595	67.70%	1.30%	11.60%	18.82%	ACTCT: 0.50%
Indica II	465	18.10%	8.20%	40.65%	25.16%	ACTCT: 6.88%; ACACT: 1.08%
Indica III	913	43.50%	3.60%	19.06%	24.75%	ACACT: 7.23%; ACTCT: 1.86%
Indica Intermediate	786	43.30%	3.60%	19.72%	30.79%	ACTCT: 1.65%; ACACT: 1.02%
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	0.00%	12.22%	8.89%	ACTCTCTCT: 2.22%; ACACT: 1.11%; ACTCT: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0429780859	A -> DEL	N	N	silent_mutation	Average:65.024; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0429780859	A -> T	LOC_Os04g49930.1	intron_variant ; MODIFIER	silent_mutation	Average:65.024; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0429780859	A -> ACTCT	LOC_Os04g49930.1	intron_variant ; MODIFIER	silent_mutation	Average:65.024; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0429780859	A -> ACACT	LOC_Os04g49930.1	intron_variant ; MODIFIER	silent_mutation	Average:65.024; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0429780859	A -> ACTCTCTCT	LOC_Os04g49930.1	intron_variant ; MODIFIER	silent_mutation	Average:65.024; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429780859	NA	3.48E-09	mr1045	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
vg0429780859	2.95E-07	2.93E-07	mr1267	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
vg0429780859	NA	3.34E-07	mr1380	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
vg0429780859	NA	6.82E-08	mr1561	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
vg0429780859	NA	4.27E-07	mr1875	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
vg0429780859	NA	3.48E-06	mr1908	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
vg0429780859	NA	3.54E-07	mr1937	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
vg0429780859	NA	2.53E-06	mr1937	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
vg0429780859	5.79E-06	5.80E-06	mr1996	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