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Detailed information for vg0113283794:

Variant ID: vg0113283794 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 13283794
Reference Allele: T	Alternative Allele: C,TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC,TGGAGTAGTCATCGGCTTAGTGAAATTTGGTAAGCCC
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AACACCAATGCTATTTGTGCTATTGTGCTGTGTTTGCATTAAAGAGCTTGGCTAGGAGTACAAGATGCACCATGGTGTTAACAGTGAAATTTGGTAAGCC[T/C,TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC,TGGAGTAGTCATCGGCTTAGTGAAATTTGGTAAGCCC]
GGAGTAGTCATCGGCTTAGAGTCAACATCGGCTTCGAAGTCCTGAGATTAGCCGATGAGAATTGTCAAGTCGTCGGTTGTCGGATTCTTGCTATATTCGG

Reverse complement sequence

CCGAATATAGCAAGAATCCGACAACCGACGACTTGACAATTCTCATCGGCTAATCTCAGGACTTCGAAGCCGATGTTGACTCTAAGCCGATGACTACTCC[A/G,GGGCTTACCAAATTTCACTAAGCCGATGACTA,GGGCTTACCAAATTTCACTAAGCCGATGACTACTCCA]
GGCTTACCAAATTTCACTGTTAACACCATGGTGCATCTTGTACTCCTAGCCAAGCTCTTTAATGCAAACACAGCACAATAGCACAAATAGCATTGGTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.10%	26.40%	1.57%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 2.88%; TGGAGTAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.04%
All Indica	2759	95.30%	0.80%	1.38%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 2.46%; TGGAGTAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.07%
All Japonica	1512	21.40%	78.20%	0.33%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.07%
Aus	269	68.40%	0.40%	10.41%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 20.82%
Indica I	595	98.30%	0.20%	1.34%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.17%
Indica II	465	97.00%	1.90%	0.65%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.43%
Indica III	913	94.10%	0.20%	0.77%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 4.71%; TGGAGTAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.22%
Indica Intermediate	786	93.30%	1.40%	2.54%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 2.80%
Temperate Japonica	767	22.30%	77.20%	0.52%	0.00%	NA
Tropical Japonica	504	27.20%	72.60%	0.00%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 0.20%
Japonica Intermediate	241	6.60%	92.90%	0.41%	0.00%	NA
VI/Aromatic	96	80.20%	9.40%	1.04%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 9.38%
Intermediate	90	60.00%	35.60%	2.22%	0.00%	TAGTCATCGGCTTAGTGAAATTTGGTAAGCCC: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113283794	T -> TAGTCATCGGCTTAGTGAAATTTGGTAAGC CC	LOC_Os01g23620.1	upstream_gene_variant ; 2308.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TAGTCATCGGCTTAGTGAAATTTGGTAAGC CC	LOC_Os01g23610.1	downstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TAGTCATCGGCTTAGTGAAATTTGGTAAGC CC	LOC_Os01g23610.2	downstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TAGTCATCGGCTTAGTGAAATTTGGTAAGC CC	LOC_Os01g23610-LOC_Os01g23620	intergenic_region ; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> C	LOC_Os01g23620.1	upstream_gene_variant ; 2309.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> C	LOC_Os01g23610.1	downstream_gene_variant ; 1593.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> C	LOC_Os01g23610.2	downstream_gene_variant ; 1593.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> C	LOC_Os01g23610-LOC_Os01g23620	intergenic_region ; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TGGAGTAGTCATCGGCTTAGTGAAATTTGG TAAGCCC	LOC_Os01g23620.1	upstream_gene_variant ; 2308.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TGGAGTAGTCATCGGCTTAGTGAAATTTGG TAAGCCC	LOC_Os01g23610.1	downstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TGGAGTAGTCATCGGCTTAGTGAAATTTGG TAAGCCC	LOC_Os01g23610.2	downstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0113283794	T -> TGGAGTAGTCATCGGCTTAGTGAAATTTGG TAAGCCC	LOC_Os01g23610-LOC_Os01g23620	intergenic_region ; MODIFIER	silent_mutation	Average:61.463; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113283794	NA	5.50E-12	Plant_height	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
vg0113283794	NA	1.37E-14	mr1062	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
vg0113283794	NA	2.17E-09	mr1322	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
vg0113283794	NA	3.66E-10	mr1623	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
vg0113283794	NA	1.97E-09	mr1648	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
vg0113283794	NA	1.31E-20	mr1010_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
vg0113283794	1.85E-06	2.57E-12	mr1030_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
vg0113283794	NA	2.06E-08	mr1030_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
vg0113283794	NA	1.20E-07	mr1164_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
vg0113283794	NA	1.24E-06	mr1173_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
vg0113283794	NA	8.66E-06	mr1296_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
vg0113283794	NA	1.58E-06	mr1330_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
vg0113283794	NA	2.60E-06	mr1355_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
vg0113283794	NA	7.82E-07	mr1358_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
vg0113283794	NA	9.06E-06	mr1444_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
vg0113283794	NA	5.70E-06	mr1452_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
vg0113283794	NA	8.93E-07	mr1568_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
vg0113283794	NA	5.06E-11	mr1576_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
vg0113283794	NA	3.09E-09	mr1709_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
vg0113283794	NA	6.24E-20	mr1712_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
vg0113283794	NA	6.69E-09	mr1749_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
vg0113283794	NA	6.67E-12	mr1761_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
vg0113283794	NA	5.70E-13	mr1770_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
vg0113283794	NA	1.05E-08	mr1821_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
vg0113283794	NA	1.51E-16	mr1836_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
vg0113283794	NA	5.08E-09	mr1946_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
vg0113283794	NA	5.08E-09	mr1948_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