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Detailed information for vg0502285091:

Variant ID: vg0502285091 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2285091
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGCATGTGAAAATAAGCTCATTTTCGCGTGCGGTCCTCTTAAATGAACCGCACGTGAAAATGAGCCTATTTTTATAGACGCGACCAGTTATGATCCGT[T/C]
TGCAATCTAAATGAGTCCGTGTCCAGAAAAATCGTCTGTGTAATAGTGAACGAGAGATATTGTTGGATCTTCATGACAGAGGTGGCGGCCCTACTAGTTC

Reverse complement sequence

GAACTAGTAGGGCCGCCACCTCTGTCATGAAGATCCAACAATATCTCTCGTTCACTATTACACAGACGATTTTTCTGGACACGGACTCATTTAGATTGCA[A/G]
ACGGATCATAACTGGTCGCGTCTATAAAAATAGGCTCATTTTCACGTGCGGTTCATTTAAGAGGACCGCACGCGAAAATGAGCTTATTTTCACATGCGGA

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	76.40%	23.40%	0.15%	0.00%	NA
All Indica	2759	98.60%	1.30%	0.07%	0.00%	NA
All Japonica	1512	31.30%	68.50%	0.20%	0.00%	NA
Aus	269	96.70%	3.00%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.40%	1.60%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.40%	0.25%	0.00%	NA
Temperate Japonica	767	7.20%	92.80%	0.00%	0.00%	NA
Tropical Japonica	504	65.50%	34.10%	0.40%	0.00%	NA
Japonica Intermediate	241	36.90%	62.70%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	1.11%	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
vg0502285091	T -> C	LOC_Os05g04790-LOC_Os05g04810	intergenic_region ; MODIFIER	silent_mutation	Average:62.818; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502285091	NA	3.03E-13	mr1741	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
vg0502285091	6.94E-06	NA	mr1301_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
vg0502285091	NA	2.36E-30	mr1423_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
vg0502285091	NA	8.90E-07	mr1423_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
vg0502285091	NA	3.62E-07	mr1555_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
vg0502285091	NA	1.72E-07	mr1570_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
vg0502285091	NA	6.20E-07	mr1596_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
vg0502285091	NA	4.98E-06	mr1695_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
vg0502285091	8.29E-07	NA	mr1705_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
vg0502285091	3.37E-06	NA	mr1705_2	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
vg0502285091	NA	6.28E-06	mr1763_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
vg0502285091	NA	7.53E-31	mr1789_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
vg0502285091	NA	3.09E-12	mr1789_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
vg0502285091	NA	6.13E-08	mr1837_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
vg0502285091	NA	2.54E-13	mr1844_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
vg0502285091	NA	9.75E-07	mr1844_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