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Detailed information for vg0613089610:

Variant ID: vg0613089610 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13089610
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGGTTCATCGGCTGGCCTGGCACCATGGCTGATGTAGCAGGTAAGGGAGTCGATGCTGGCGCCGTCGGCTGAGTTGTGGGTGCAACGGACGGAACTGC[T/C]
TGAATAGATGGCTGAACATCGGTGATCAAAGATCGATAATTTGGGAAGACACCTCCTTGCAAATAAACTGGGCCTGCAGCCTGATGCTCAGCTATTGAAC

Reverse complement sequence

GTTCAATAGCTGAGCATCAGGCTGCAGGCCCAGTTTATTTGCAAGGAGGTGTCTTCCCAAATTATCGATCTTTGATCACCGATGTTCAGCCATCTATTCA[A/G]
GCAGTTCCGTCCGTTGCACCCACAACTCAGCCGACGGCGCCAGCATCGACTCCCTTACCTGCTACATCAGCCATGGTGCCAGGCCAGCCGATGAACCCTC

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	51.40%	0.20%	5.21%	43.21%	NA
All Indica	2759	22.90%	0.30%	7.94%	68.79%	NA
All Japonica	1512	97.90%	0.00%	0.07%	2.05%	NA
Aus	269	62.50%	0.00%	8.55%	29.00%	NA
Indica I	595	21.70%	0.50%	4.03%	73.78%	NA
Indica II	465	8.40%	0.20%	4.52%	86.88%	NA
Indica III	913	24.00%	0.00%	14.24%	61.77%	NA
Indica Intermediate	786	31.30%	0.60%	5.60%	62.47%	NA
Temperate Japonica	767	96.70%	0.00%	0.00%	3.26%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	57.80%	0.00%	3.33%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613089610	T -> C	LOC_Os06g22520.1	synonymous_variant ; p.Gln195Gln; LOW	synonymous_codon	Average:43.534; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0613089610	T -> DEL	LOC_Os06g22520.1	N	frameshift_variant	Average:43.534; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613089610	NA	4.45E-06	mr1104	Ind_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
vg0613089610	4.59E-06	3.62E-06	mr1268	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
vg0613089610	NA	7.69E-11	mr1172_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
vg0613089610	NA	3.15E-07	mr1604_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
vg0613089610	NA	6.64E-06	mr1992_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