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Detailed information for vg0418071347:

Variant ID: vg0418071347 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 18071347
Reference Allele: A	Alternative Allele: G,ACTCCCTCCGTTTCACAATGTGAGACTT
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TATATTTACGATTACTTCATATTAACTAGGCACACCTTGTGATACAACAAAGTTTTCAGAGGGACATACTACTACGTAACAAACATAATCTATAGCTACT[A/G,ACTCCCTCCGTTTCACAATGTGAGACTT]
TATAAATGGAGATACAGTAAGACAAATGTTATTGGCATATAAATAGAAGCACTCGCAATGGAACAACAAAACATGTAGTAATTGTGCGGTCATCTAGCAA

Reverse complement sequence

TTGCTAGATGACCGCACAATTACTACATGTTTTGTTGTTCCATTGCGAGTGCTTCTATTTATATGCCAATAACATTTGTCTTACTGTATCTCCATTTATA[T/C,AAGTCTCACATTGTGAAACGGAGGGAGT]
AGTAGCTATAGATTATGTTTGTTACGTAGTAGTATGTCCCTCTGAAAACTTTGTTGTATCACAAGGTGTGCCTAGTTAATATGAAGTAATCGTAAATATA

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	88.80%	8.00%	3.17%	0.02%	NA
All Indica	2759	98.80%	0.90%	0.22%	0.00%	NA
All Japonica	1512	69.10%	21.60%	9.26%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.70%	3.90%	0.43%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	98.70%	0.90%	0.38%	0.00%	NA
Temperate Japonica	767	97.80%	0.10%	2.09%	0.00%	NA
Tropical Japonica	504	35.50%	50.80%	13.49%	0.20%	NA
Japonica Intermediate	241	48.10%	28.60%	23.24%	0.00%	NA
VI/Aromatic	96	84.40%	14.60%	1.04%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0418071347	A -> ACTCCCTCCGTTTCACAATGTGAGACTT	LOC_Os04g30270.1	intron_variant ; MODIFIER	N	Average:49.659; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0418071347	A -> DEL	N	N	silent_mutation	Average:49.659; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0418071347	A -> G	LOC_Os04g30270.1	intron_variant ; MODIFIER	silent_mutation	Average:49.659; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418071347	3.58E-07	NA	mr1076	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
vg0418071347	1.27E-06	NA	mr1082	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
vg0418071347	NA	3.34E-06	mr1082	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
vg0418071347	7.09E-06	NA	mr1104	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
vg0418071347	3.58E-08	NA	mr1226	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
vg0418071347	NA	1.37E-08	mr1408	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
vg0418071347	1.12E-06	NA	mr1411	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
vg0418071347	NA	2.13E-06	mr1522	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
vg0418071347	2.44E-07	NA	mr1560	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
vg0418071347	NA	6.92E-06	mr1560	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
vg0418071347	NA	3.50E-06	mr1077_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
vg0418071347	3.84E-06	3.84E-06	mr1146_2	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
vg0418071347	NA	6.65E-06	mr1220_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
vg0418071347	NA	2.74E-06	mr1289_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
vg0418071347	NA	2.07E-06	mr1479_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
vg0418071347	NA	1.44E-07	mr1498_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
vg0418071347	NA	1.31E-08	mr1502_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
vg0418071347	NA	9.14E-06	mr1759_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
vg0418071347	NA	7.93E-07	mr1929_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