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Detailed information for vg0432718715:

Variant ID: vg0432718715 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32718715
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAGTTAGCACCCCGCTACATCGGCCCCTACCTCATAACCGCCAGACGTGGCGAAGTGGCTTATCAGCTTGAGTTACCTGAAGGTCTCGCAGATGTGCA[T/C]
AACGTGTTTCACGTATCCCAGTTAAAGAAATGTCTTCGAGTTCCAGAAGAGCAAGTTCCCCTGGGTAATATCGTGCTGGAAAAGAATCTGACCTACAAGG

Reverse complement sequence

CCTTGTAGGTCAGATTCTTTTCCAGCACGATATTACCCAGGGGAACTTGCTCTTCTGGAACTCGAAGACATTTCTTTAACTGGGATACGTGAAACACGTT[A/G]
TGCACATCTGCGAGACCTTCAGGTAACTCAAGCTGATAAGCCACTTCGCCACGTCTGGCGGTTATGAGGTAGGGGCCGATGTAGCGGGGTGCTAACTTGC

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	21.50%	2.40%	5.56%	70.59%	NA
All Indica	2759	3.90%	3.20%	5.55%	87.35%	NA
All Japonica	1512	53.10%	0.80%	5.16%	40.94%	NA
Aus	269	25.30%	1.90%	6.69%	66.17%	NA
Indica I	595	4.00%	3.00%	4.20%	88.74%	NA
Indica II	465	6.90%	2.20%	5.16%	85.81%	NA
Indica III	913	1.60%	4.30%	6.79%	87.29%	NA
Indica Intermediate	786	4.60%	2.80%	5.34%	87.28%	NA
Temperate Japonica	767	76.70%	0.30%	6.26%	16.82%	NA
Tropical Japonica	504	31.20%	1.60%	4.96%	62.30%	NA
Japonica Intermediate	241	24.10%	0.80%	2.07%	73.03%	NA
VI/Aromatic	96	10.40%	4.20%	9.38%	76.04%	NA
Intermediate	90	30.00%	2.20%	5.56%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432718715	T -> C	LOC_Os04g55020.1	synonymous_variant ; p.His1680His; LOW	synonymous_codon	Average:8.073; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0432718715	T -> DEL	LOC_Os04g55020.1	N	frameshift_variant	Average:8.073; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432718715	3.87E-06	1.94E-07	mr1022	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
vg0432718715	NA	7.43E-07	mr1040	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
vg0432718715	8.74E-07	NA	mr1079	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
vg0432718715	NA	5.39E-06	mr1114	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
vg0432718715	3.90E-06	1.94E-07	mr1116	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
vg0432718715	NA	3.91E-06	mr1117	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
vg0432718715	NA	7.17E-06	mr1240	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
vg0432718715	4.79E-06	NA	mr1489	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
vg0432718715	6.29E-06	NA	mr1491	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
vg0432718715	4.79E-06	NA	mr1491	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
vg0432718715	NA	3.83E-06	mr1745	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
vg0432718715	NA	5.15E-06	mr1917	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
vg0432718715	NA	7.63E-08	mr1794_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