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Detailed information for vg1022632091:

Variant ID: vg1022632091 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 22632091
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, C: 0.42, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCATAGCTAGTCTTGTGCGGCACTGTCTCCGGCGTCTCCTGTGCGGCGCCTCTGTCGTGGCGGCTCCTCCTCCGTCTCCGTCTCCGTCTCCGGCGCCG[C/G]
CCTCTTCTGCACGACGACGACGGGACTTGCTGTTCGGTTGGCATCGGCTAACAAGACTGCGGAGAACGCTTGTGCTTCCGCAATCTCCGCCTCGGCCGTC

Reverse complement sequence

GACGGCCGAGGCGGAGATTGCGGAAGCACAAGCGTTCTCCGCAGTCTTGTTAGCCGATGCCAACCGAACAGCAAGTCCCGTCGTCGTCGTGCAGAAGAGG[G/C]
CGGCGCCGGAGACGGAGACGGAGACGGAGGAGGAGCCGCCACGACAGAGGCGCCGCACAGGAGACGCCGGAGACAGTGCCGCACAAGACTAGCTATGGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.40%	11.20%	1.27%	51.18%	NA
All Indica	2759	3.70%	11.80%	2.10%	82.35%	NA
All Japonica	1512	95.80%	0.30%	0.07%	3.77%	NA
Aus	269	14.10%	64.30%	0.00%	21.56%	NA
Indica I	595	5.40%	3.50%	2.52%	88.57%	NA
Indica II	465	3.40%	28.00%	1.29%	67.31%	NA
Indica III	913	1.40%	5.50%	1.97%	91.13%	NA
Indica Intermediate	786	5.30%	15.90%	2.42%	76.34%	NA
Temperate Japonica	767	99.20%	0.10%	0.13%	0.52%	NA
Tropical Japonica	504	89.10%	0.80%	0.00%	10.12%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	86.50%	11.50%	0.00%	2.08%	NA
Intermediate	90	51.10%	14.40%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1022632091	C -> G	LOC_Os10g42072.1	missense_variant ; p.Ala250Pro; MODERATE	nonsynonymous_codon ; A250P	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	unknown	unknown	TOLERATED	1.00
vg1022632091	C -> DEL	LOC_Os10g42072.1	N	frameshift_variant	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
vg1022632091	NA	5.04E-07	mr1382	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
vg1022632091	NA	2.40E-07	mr1574	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
vg1022632091	NA	4.38E-09	mr1866	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