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Detailed information for vg0900339005:

Variant ID: vg0900339005 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 339005
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGATAGCCTTGTCCACAAGTTTCTCAAAGTTCTCATAGACTTCGGAGATCAGCTAGTTGGTCAACTCATTATCAAGACCATACAAAAACTTCTCCTGC[C/T]
TCTCGGCATCGATGCGCATGTCCTCAGGAGCGTAGCGCGCGAGGCGATTGAACTCATGCAGATACTCTGTAACTGTCCTGGTCCCTTGTTGCAGTGCACG

Reverse complement sequence

CGTGCACTGCAACAAGGGACCAGGACAGTTACAGAGTATCTGCATGAGTTCAATCGCCTCGCGCGCTACGCTCCTGAGGACATGCGCATCGATGCCGAGA[G/A]
GCAGGAGAAGTTTTTGTATGGTCTTGATAATGAGTTGACCAACTAGCTGATCTCCGAAGTCTATGAGAACTTTGAGAAACTTGTGGACAAGGCTATCCGT

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	34.00%	5.40%	50.66%	9.86%	NA
All Indica	2759	6.90%	8.30%	77.46%	7.36%	NA
All Japonica	1512	83.10%	0.10%	0.60%	16.20%	NA
Aus	269	3.70%	9.30%	80.67%	6.32%	NA
Indica I	595	13.40%	5.40%	68.40%	12.77%	NA
Indica II	465	4.70%	12.30%	74.84%	8.17%	NA
Indica III	913	3.00%	6.50%	88.28%	2.30%	NA
Indica Intermediate	786	7.90%	10.20%	73.28%	8.65%	NA
Temperate Japonica	767	68.80%	0.30%	0.39%	30.51%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	94.20%	0.00%	1.24%	4.56%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	66.70%	2.20%	30.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900339005	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900339005	C -> T	LOC_Os09g01460.1	downstream_gene_variant ; 1167.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900339005	C -> T	LOC_Os09g01450.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900339005	2.10E-06	2.66E-07	mr1071_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
vg0900339005	NA	5.93E-06	mr1080_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
vg0900339005	2.51E-07	7.59E-08	mr1203_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
vg0900339005	NA	1.76E-06	mr1613_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
vg0900339005	7.15E-07	3.25E-07	mr1619_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
vg0900339005	NA	1.26E-06	mr1795_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
vg0900339005	NA	2.29E-07	mr1821_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
vg0900339005	NA	2.11E-07	mr1913_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