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Detailed information for vg0225356942:

Variant ID: vg0225356942 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25356942
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCTGTGCTTGGGATTTACCAGCATTTGGGCTTAAAAGGTGCTGAATCTCTCCACCACTTCCTGGGACTGGGAGAAATTGGAATTTTCTTAGCCTCTTA[G/C]
TTCTCAGGAATTGCAGCCTCATCTCTACTTCTTTCATAGTAGGTCTATCTCCTCCTCTGAGTTTCAAGCATGCCTCTGTAAGTGAGGCAATATCATCAAT

Reverse complement sequence

ATTGATGATATTGCCTCACTTACAGAGGCATGCTTGAAACTCAGAGGAGGAGATAGACCTACTATGAAAGAAGTAGAGATGAGGCTGCAATTCCTGAGAA[C/G]
TAAGAGGCTAAGAAAATTCCAATTTCTCCCAGTCCCAGGAAGTGGTGGAGAGATTCAGCACCTTTTAAGCCCAAATGCTGGTAAATCCCAAGCACAGAAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	1.00%	0.66%	1.61%	NA
All Indica	2759	96.10%	0.50%	0.72%	2.68%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	85.10%	11.20%	3.35%	0.37%	NA
Indica I	595	99.70%	0.00%	0.17%	0.17%	NA
Indica II	465	98.70%	0.00%	0.22%	1.08%	NA
Indica III	913	92.60%	1.10%	0.88%	5.48%	NA
Indica Intermediate	786	95.90%	0.50%	1.27%	2.29%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	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
vg0225356942	G -> DEL	LOC_Os02g42160.1	N	frameshift_variant	Average:31.043; most accessible tissue: Zhenshan97 flower, score: 39.624	N	N	N	N
vg0225356942	G -> C	LOC_Os02g42160.1	missense_variant ; p.Thr617Ser; MODERATE	nonsynonymous_codon ; T617S	Average:31.043; most accessible tissue: Zhenshan97 flower, score: 39.624	benign	0.076	TOLERATED	0.23

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225356942	NA	8.28E-06	mr1631_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