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Detailed information for vg0407783729:

Variant ID: vg0407783729 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7783729
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.17, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCAGTTCAGAACTTCATCAGATAGGACTGTCAGAAATCCCCATCGCCAGTGAATTCGGTGACGTGTTTCCGGAAGAACTACCCGGTATGCCGCCCAAG[T/C]
GGGAGATCGAGTTCCGGATAGATCTTGCTCCAGGAACAACTCCTCTGTACAAACGGCCCTACCGTATGGCAGCAAATGAACTTGCCGAAGTCAAGAAGCA

Reverse complement sequence

TGCTTCTTGACTTCGGCAAGTTCATTTGCTGCCATACGGTAGGGCCGTTTGTACAGAGGAGTTGTTCCTGGAGCAAGATCTATCCGGAACTCGATCTCCC[A/G]
CTTGGGCGGCATACCGGGTAGTTCTTCCGGAAACACGTCACCGAATTCACTGGCGATGGGGATTTCTGACAGTCCTATCTGATGAAGTTCTGAACTGCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.40%	2.90%	44.99%	10.69%	NA
All Indica	2759	27.10%	3.20%	66.15%	3.52%	NA
All Japonica	1512	73.80%	1.30%	4.56%	20.37%	NA
Aus	269	7.40%	0.00%	58.74%	33.83%	NA
Indica I	595	29.20%	1.50%	65.21%	4.03%	NA
Indica II	465	21.30%	4.50%	73.55%	0.65%	NA
Indica III	913	26.60%	3.90%	63.96%	5.48%	NA
Indica Intermediate	786	29.60%	2.80%	65.01%	2.54%	NA
Temperate Japonica	767	96.50%	0.10%	0.91%	2.48%	NA
Tropical Japonica	504	41.10%	2.20%	8.53%	48.21%	NA
Japonica Intermediate	241	70.10%	2.90%	7.88%	19.09%	NA
VI/Aromatic	96	27.10%	28.10%	41.67%	3.12%	NA
Intermediate	90	51.10%	4.40%	37.78%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407783729	T -> C	LOC_Os04g13930.1	missense_variant ; p.Trp747Arg; MODERATE	nonsynonymous_codon ; W747R	Average:14.505; most accessible tissue: Zhenshan97 root, score: 29.203	probably damaging	-3.32	TOLERATED	1.00
vg0407783729	T -> DEL	LOC_Os04g13930.1	N	frameshift_variant	Average:14.505; most accessible tissue: Zhenshan97 root, score: 29.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407783729	NA	3.27E-06	mr1047	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
vg0407783729	NA	1.09E-12	mr1149	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
vg0407783729	NA	1.28E-07	mr1162	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
vg0407783729	NA	2.05E-06	mr1291	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
vg0407783729	NA	6.11E-06	mr1446	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
vg0407783729	NA	1.02E-12	mr1471	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
vg0407783729	NA	9.52E-07	mr1471	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
vg0407783729	NA	4.64E-10	mr1630	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
vg0407783729	NA	2.55E-08	mr1704	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
vg0407783729	NA	7.78E-09	mr1746	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
vg0407783729	NA	9.50E-10	mr1790	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
vg0407783729	NA	3.81E-07	mr1815	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
vg0407783729	NA	1.46E-14	mr1982	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
vg0407783729	NA	1.90E-17	mr1682_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