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Detailed information for vg0225359930:

Variant ID: vg0225359930 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25359930
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, T: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGGGTAGGAGATGCCATCGACTTCCCCGCAGCTAGAGGGGCAGTGAGCGAGGGAGTCATTAGAAGGGACAATCAAGAGCCCTCCACCAACTCCATAGA[C/T]
TGAAGCCAATACTCGTGGCGTAGCTGCCGAGCACACCAGCACAAAAGAAGTGGCACAAACTGCCAGAAAGCTCGAGCTCATCTTTGCGCCAGCCGGCTTG

Reverse complement sequence

CAAGCCGGCTGGCGCAAAGATGAGCTCGAGCTTTCTGGCAGTTTGTGCCACTTCTTTTGTGCTGGTGTGCTCGGCAGCTACGCCACGAGTATTGGCTTCA[G/A]
TCTATGGAGTTGGTGGAGGGCTCTTGATTGTCCCTTCTAATGACTCCCTCGCTCACTGCCCCTCTAGCTGCGGGGAAGTCGATGGCATCTCCTACCCCTT

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	35.80%	22.20%	0.68%	41.30%	NA
All Indica	2759	17.00%	25.40%	0.76%	56.80%	NA
All Japonica	1512	72.60%	19.90%	0.60%	6.94%	NA
Aus	269	7.10%	3.00%	0.00%	89.96%	NA
Indica I	595	7.10%	57.30%	0.34%	35.29%	NA
Indica II	465	7.10%	25.60%	1.72%	65.59%	NA
Indica III	913	31.00%	6.80%	0.55%	61.66%	NA
Indica Intermediate	786	14.10%	22.90%	0.76%	62.21%	NA
Temperate Japonica	767	80.70%	17.30%	0.65%	1.30%	NA
Tropical Japonica	504	66.30%	20.60%	0.20%	12.90%	NA
Japonica Intermediate	241	59.80%	26.60%	1.24%	12.45%	NA
VI/Aromatic	96	63.50%	25.00%	0.00%	11.46%	NA
Intermediate	90	51.10%	16.70%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0225359930	C -> T	LOC_Os02g42160.1	missense_variant ; p.Val28Ile; MODERATE	nonsynonymous_codon ; V28I	Average:76.004; most accessible tissue: Callus, score: 97.453	unknown	unknown	TOLERATED	0.29
vg0225359930	C -> DEL	LOC_Os02g42160.1	N	frameshift_variant	Average:76.004; most accessible tissue: Callus, score: 97.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225359930	NA	5.02E-07	mr1069	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
vg0225359930	NA	4.90E-06	mr1074	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
vg0225359930	NA	1.29E-07	mr1077	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
vg0225359930	3.59E-07	3.59E-07	mr1270	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
vg0225359930	NA	1.55E-06	mr1619	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
vg0225359930	NA	2.04E-07	mr1861	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
vg0225359930	NA	3.66E-07	mr1962	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
vg0225359930	NA	4.72E-07	mr1074_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
vg0225359930	NA	5.02E-06	mr1095_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
vg0225359930	NA	4.45E-06	mr1148_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
vg0225359930	NA	2.66E-06	mr1150_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
vg0225359930	NA	1.21E-06	mr1222_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
vg0225359930	NA	3.22E-08	mr1558_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
vg0225359930	NA	9.88E-06	mr1918_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