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Detailed information for vg0520975375:

Variant ID: vg0520975375 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20975375
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGTCATCCTTTATGTGAATGATAAATGGACCATACATATATTTTTTTAATTCTAATGCCACGTAACCGCCACGTCAACGCCACGTGTAAGAAAGACC[T/C]
GGTTAGCACCGTCACGTAGGTGCCACGTCAGCAAAACCGCCCTCTAAAACCGCCGAGGGAGTCAAATTGTACTGGTTTTAAGAGTTGGTGGTCTAGATAT

Reverse complement sequence

ATATCTAGACCACCAACTCTTAAAACCAGTACAATTTGACTCCCTCGGCGGTTTTAGAGGGCGGTTTTGCTGACGTGGCACCTACGTGACGGTGCTAACC[A/G]
GGTCTTTCTTACACGTGGCGTTGACGTGGCGGTTACGTGGCATTAGAATTAAAAAAATATATGTATGGTCCATTTATCATTCACATAAAGGATGACATGC

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	25.90%	10.40%	2.45%	61.28%	NA
All Indica	2759	3.70%	0.40%	0.51%	95.36%	NA
All Japonica	1512	60.10%	31.20%	6.61%	2.12%	NA
Aus	269	32.30%	0.00%	0.00%	67.66%	NA
Indica I	595	0.50%	0.30%	0.50%	98.66%	NA
Indica II	465	2.60%	0.60%	0.65%	96.13%	NA
Indica III	913	6.80%	0.10%	0.00%	93.10%	NA
Indica Intermediate	786	3.20%	0.80%	1.02%	95.04%	NA
Temperate Japonica	767	33.80%	52.50%	10.17%	3.52%	NA
Tropical Japonica	504	95.80%	1.20%	2.38%	0.60%	NA
Japonica Intermediate	241	69.30%	25.70%	4.15%	0.83%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	36.70%	8.90%	1.11%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0520975375	T -> DEL	N	N	silent_mutation	Average:59.41; most accessible tissue: Callus, score: 78.593	N	N	N	N
vg0520975375	T -> C	LOC_Os05g35320.1	upstream_gene_variant ; 2503.0bp to feature; MODIFIER	silent_mutation	Average:59.41; most accessible tissue: Callus, score: 78.593	N	N	N	N
vg0520975375	T -> C	LOC_Os05g35330.1	downstream_gene_variant ; 1045.0bp to feature; MODIFIER	silent_mutation	Average:59.41; most accessible tissue: Callus, score: 78.593	N	N	N	N
vg0520975375	T -> C	LOC_Os05g35340.1	downstream_gene_variant ; 3159.0bp to feature; MODIFIER	silent_mutation	Average:59.41; most accessible tissue: Callus, score: 78.593	N	N	N	N
vg0520975375	T -> C	LOC_Os05g35330-LOC_Os05g35340	intergenic_region ; MODIFIER	silent_mutation	Average:59.41; most accessible tissue: Callus, score: 78.593	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520975375	NA	4.11E-12	Plant_height	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0520975375	NA	3.72E-17	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0520975375	NA	5.05E-11	Spikelet_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0520975375	NA	6.10E-07	mr1077	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
vg0520975375	NA	5.31E-08	mr1164	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
vg0520975375	NA	2.05E-06	mr1202	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
vg0520975375	NA	1.18E-06	mr1205	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
vg0520975375	NA	4.63E-07	mr1252	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
vg0520975375	NA	1.10E-06	mr1252	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
vg0520975375	NA	1.16E-07	mr1271	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
vg0520975375	NA	4.65E-09	mr1271	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
vg0520975375	NA	5.28E-06	mr1330	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
vg0520975375	NA	2.73E-06	mr1548	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
vg0520975375	NA	8.79E-06	mr1550	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
vg0520975375	NA	7.84E-06	mr1596	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
vg0520975375	NA	5.13E-07	mr1617	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
vg0520975375	NA	8.35E-08	mr1627	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
vg0520975375	NA	6.34E-07	mr1763	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
vg0520975375	NA	6.67E-06	mr1775	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
vg0520975375	NA	6.98E-06	mr1164_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
vg0520975375	NA	1.16E-08	mr1576_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
vg0520975375	NA	1.90E-06	mr1588_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
vg0520975375	NA	1.18E-11	mr1709_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
vg0520975375	NA	1.96E-07	mr1748_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
vg0520975375	NA	3.32E-09	mr1805_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
vg0520975375	2.34E-06	2.33E-06	mr1919_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