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Detailed information for vg0602930529:

Variant ID: vg0602930529 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2930529
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATTGGGTGTCTGAGCCATGACCTTGGTGTTAACAATCTCTCGTTGGTTCCATCTACATTGGAAGTGCCTTACCATTGCTTTGTATTGGGCTCAGTATG[T/C]
AGAGCTAGCTCACCACCAGTACCACTTTGGAGAGTGGCAGTTCCATGGTACAGCGATCAGGTCTTTTCAGGTTCTCGGCCCTCGCCATGGCCTGATCCAT

Reverse complement sequence

ATGGATCAGGCCATGGCGAGGGCCGAGAACCTGAAAAGACCTGATCGCTGTACCATGGAACTGCCACTCTCCAAAGTGGTACTGGTGGTGAGCTAGCTCT[A/G]
CATACTGAGCCCAATACAAAGCAATGGTAAGGCACTTCCAATGTAGATGGAACCAACGAGAGATTGTTAACACCAAGGTCATGGCTCAGACACCCAATCA

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	53.50%	1.00%	2.35%	43.21%	NA
All Indica	2759	32.30%	0.50%	3.52%	63.61%	NA
All Japonica	1512	99.40%	0.00%	0.07%	0.53%	NA
Aus	269	4.80%	1.10%	3.72%	90.33%	NA
Indica I	595	32.80%	0.20%	3.03%	64.03%	NA
Indica II	465	74.00%	0.20%	1.94%	23.87%	NA
Indica III	913	6.40%	0.10%	3.40%	90.14%	NA
Indica Intermediate	786	37.50%	1.50%	4.96%	55.98%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	51.00%	26.00%	3.12%	19.79%	NA
Intermediate	90	78.90%	2.20%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0602930529	T -> C	LOC_Os06g06310.1	synonymous_variant ; p.Cys380Cys; LOW	synonymous_codon	Average:32.737; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0602930529	T -> DEL	LOC_Os06g06310.1	N	frameshift_variant	Average:32.737; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602930529	NA	9.63E-07	mr1157	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
vg0602930529	NA	4.68E-08	mr1446	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
vg0602930529	NA	3.36E-09	mr1989	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
vg0602930529	2.56E-06	NA	mr1836_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