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Detailed information for vg0921007352:

Variant ID: vg0921007352 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21007352
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGGAGATGGGGCTTCTCACCCCGGGTGAACCGGTCGGGGATGCGGCGGTGGAGGCTTATGCAAAGTCCTTCGACACACCGCTTCCGTCGCATGTCAT[T/C]
GCCGGTCTGCGGGTGCTCACACGCCTGGATGGAGTGCACGACATCCCGGTGCCAGGAGAGGAAGGAACCACCACAACGGCGGTGGTCTGAGGCACGCGCT

Reverse complement sequence

AGCGCGTGCCTCAGACCACCGCCGTTGTGGTGGTTCCTTCCTCTCCTGGCACCGGGATGTCGTGCACTCCATCCAGGCGTGTGAGCACCCGCAGACCGGC[A/G]
ATGACATGCGACGGAAGCGGTGTGTCGAAGGACTTTGCATAAGCCTCCACCGCCGCATCCCCGACCGGTTCACCCGGGGTGAGAAGCCCCATCTCCTCCA

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	49.70%	13.10%	6.52%	30.66%	NA
All Indica	2759	21.70%	18.30%	7.87%	52.16%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	32.30%	35.30%	32.34%	0.00%	NA
Indica I	595	15.80%	22.70%	4.87%	56.64%	NA
Indica II	465	7.10%	19.60%	12.04%	61.29%	NA
Indica III	913	28.40%	11.10%	8.98%	51.59%	NA
Indica Intermediate	786	27.10%	22.50%	6.36%	44.02%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	74.40%	10.00%	4.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0921007352	T -> DEL	LOC_Os09g36400.1	N	frameshift_variant	Average:11.172; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N
vg0921007352	T -> C	LOC_Os09g36400.1	synonymous_variant ; p.Ile567Ile; LOW	synonymous_codon	Average:11.172; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921007352	NA	8.29E-06	mr1011	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
vg0921007352	NA	2.10E-06	mr1627	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
vg0921007352	NA	5.88E-06	mr1031_2	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
vg0921007352	4.05E-06	5.03E-10	mr1268_2	Ind_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
vg0921007352	NA	5.35E-09	mr1319_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
vg0921007352	NA	1.46E-12	mr1521_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