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Detailed information for vg1020772860:

Variant ID: vg1020772860 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20772860
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGTGGCTAGAGCTTCGGCCCAGTAAGGAGGCATGGATGCTTGTATGAGTAGGGTGCGAATGGAATTGTTGATTGTGCGAAGCATGCGTTCGGCTTTGC[T/C]
GTTTTGAGGAGAAGTGTAAGGACAGGATAAGCGAAGCAAGGTTCCACGGCTAGCGAGAAACGAGGTAGTGGCTTGGTTAACAAATTCGGTACCATTATCC

Reverse complement sequence

GGATAATGGTACCGAATTTGTTAACCAAGCCACTACCTCGTTTCTCGCTAGCCGTGGAACCTTGCTTCGCTTATCCTGTCCTTACACTTCTCCTCAAAAC[A/G]
GCAAAGCCGAACGCATGCTTCGCACAATCAACAATTCCATTCGCACCCTACTCATACAAGCATCCATGCCTCCTTACTGGGCCGAAGCTCTAGCCACAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.10%	35.60%	0.32%	0.00%	NA
All Indica	2759	97.60%	2.20%	0.14%	0.00%	NA
All Japonica	1512	3.90%	95.60%	0.53%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	95.10%	4.50%	0.34%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.30%	0.50%	0.11%	0.00%	NA
Indica Intermediate	786	96.60%	3.30%	0.13%	0.00%	NA
Temperate Japonica	767	2.50%	96.50%	1.04%	0.00%	NA
Tropical Japonica	504	5.00%	95.00%	0.00%	0.00%	NA
Japonica Intermediate	241	6.20%	93.80%	0.00%	0.00%	NA
VI/Aromatic	96	79.20%	20.80%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	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
vg1020772860	T -> C	LOC_Os10g38970.1	intron_variant ; MODIFIER	silent_mutation	Average:14.705; most accessible tissue: Zhenshan97 flower, score: 33.783	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020772860	NA	1.04E-19	mr1021	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
vg1020772860	NA	2.10E-20	mr1477	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
vg1020772860	NA	1.15E-52	mr1558	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
vg1020772860	NA	8.20E-11	mr1578	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
vg1020772860	NA	5.69E-14	mr1726	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
vg1020772860	NA	2.21E-06	mr1761	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
vg1020772860	NA	2.26E-12	mr1819	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
vg1020772860	NA	6.69E-16	mr1950	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
vg1020772860	NA	1.04E-18	mr1167_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
vg1020772860	NA	1.53E-43	mr1509_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
vg1020772860	NA	5.05E-67	mr1558_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
vg1020772860	NA	4.49E-19	mr1578_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
vg1020772860	NA	4.83E-20	mr1581_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
vg1020772860	NA	4.06E-08	mr1819_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
vg1020772860	NA	8.76E-14	mr1950_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