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Detailed information for vg0724707548:

Variant ID: vg0724707548 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 24707548
Reference Allele: ACT	Alternative Allele: GCT,A
Primary Allele: ACT	Secondary Allele: GCT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATTTACTCTTATAGCTTATTGTACGTAGCCAAAATTTAAATTTTTAAATTTATTTTTGGGTTTTGTTCCATCGTACTTTACTTTTTTTTTCAACATTT[ACT/GCT,A]
TTTAAACCACAAATAACACACTATAACATCATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT

Reverse complement sequence

ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGATGTTATAGTGTGTTATTTGTGGTTTAAA[AGT/AGC,T]
AAATGTTGAAAAAAAAAGTAAAGTACGATGGAACAAAACCCAAAAATAAATTTAAAAATTTAAATTTTGGCTACGTACAATAAGCTATAAGAGTAAATGG

Allele Frequencies:

Populations	Population Size	Frequency of ACT(primary allele)	Frequency of GCT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.40%	3.20%	9.42%	62.80%	A: 0.23%
All Indica	2759	9.60%	4.20%	11.53%	74.66%	A: 0.04%
All Japonica	1512	48.60%	1.40%	4.89%	44.51%	A: 0.60%
Aus	269	42.00%	2.60%	11.52%	43.87%	NA
Indica I	595	25.50%	2.90%	8.24%	63.36%	NA
Indica II	465	2.80%	1.70%	10.97%	84.52%	NA
Indica III	913	2.20%	6.80%	14.68%	76.34%	NA
Indica Intermediate	786	10.10%	3.70%	10.69%	75.45%	A: 0.13%
Temperate Japonica	767	90.00%	0.30%	1.96%	7.82%	NA
Tropical Japonica	504	2.00%	3.40%	7.74%	85.71%	A: 1.19%
Japonica Intermediate	241	14.50%	0.80%	8.30%	75.10%	A: 1.24%
VI/Aromatic	96	15.60%	2.10%	11.46%	70.83%	NA
Intermediate	90	27.80%	4.40%	12.22%	54.44%	A: 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
vg0724707548	ACT -> A	LOC_Os07g41230.1	downstream_gene_variant ; 3755.0bp to feature; MODIFIER	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0724707548	ACT -> A	LOC_Os07g41230-LOC_Os07g41240	intergenic_region ; MODIFIER	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0724707548	ACT -> DEL	N	N	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0724707548	ACT -> GCT	LOC_Os07g41230.1	downstream_gene_variant ; 3754.0bp to feature; MODIFIER	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0724707548	ACT -> GCT	LOC_Os07g41230-LOC_Os07g41240	intergenic_region ; MODIFIER	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724707548	NA	4.82E-14	Grain_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0724707548	NA	4.51E-09	mr1486	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
vg0724707548	NA	9.01E-11	mr1549	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
vg0724707548	NA	3.99E-13	mr1563	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
vg0724707548	NA	5.89E-10	mr1570	Jap_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
vg0724707548	NA	4.79E-10	mr1580	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
vg0724707548	NA	3.80E-08	mr1757	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
vg0724707548	NA	8.14E-08	mr1825	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
vg0724707548	NA	2.15E-09	mr1880	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
vg0724707548	NA	5.34E-10	mr1959	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
vg0724707548	NA	1.17E-07	mr1156_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
vg0724707548	NA	1.47E-07	mr1310_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
vg0724707548	NA	1.91E-10	mr1486_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
vg0724707548	NA	4.83E-07	mr1521_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
vg0724707548	1.12E-06	1.12E-10	mr1563_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
vg0724707548	NA	5.84E-11	mr1580_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
vg0724707548	NA	1.11E-07	mr1733_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
vg0724707548	NA	2.54E-10	mr1825_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
vg0724707548	NA	2.41E-06	mr1966_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