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Detailed information for vg1012696203:

Variant ID: vg1012696203 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12696203
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.53, T: 0.44, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

GAACAGATTGCAGCTATATTTGGGCCATCTCAACCGGTTGTCGAGCCGATTCAATCGACACCAATTAGGCAGCAAGTGGTTCAGCCGATTAGGCAGCAGA[T/C]
GGTTCCACAAATACCGGCAGGACAGAGAACACCTATTATTCAGCAAAATCAGCCTGTTGGAGCTCAGTTTGTTCCTAAACAGCAGATACATAATGTGCAA

Reverse complement sequence

TTGCACATTATGTATCTGCTGTTTAGGAACAAACTGAGCTCCAACAGGCTGATTTTGCTGAATAATAGGTGTTCTCTGTCCTGCCGGTATTTGTGGAACC[A/G]
TCTGCTGCCTAATCGGCTGAACCACTTGCTGCCTAATTGGTGTCGATTGAATCGGCTCGACAACCGGTTGAGATGGCCCAAATATAGCTGCAATCTGTTC

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	54.30%	30.70%	0.76%	14.28%	NA
All Indica	2759	73.10%	2.30%	1.23%	23.38%	NA
All Japonica	1512	11.10%	88.70%	0.00%	0.20%	NA
Aus	269	91.10%	1.10%	0.00%	7.81%	NA
Indica I	595	93.40%	1.80%	0.50%	4.20%	NA
Indica II	465	65.80%	3.40%	1.08%	29.68%	NA
Indica III	913	68.50%	1.30%	1.53%	28.70%	NA
Indica Intermediate	786	67.40%	3.10%	1.53%	27.99%	NA
Temperate Japonica	767	2.70%	97.10%	0.00%	0.13%	NA
Tropical Japonica	504	19.40%	80.40%	0.00%	0.20%	NA
Japonica Intermediate	241	20.30%	79.30%	0.00%	0.41%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	50.00%	41.10%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012696203	T -> C	LOC_Os10g24700.1	missense_variant ; p.Met179Thr; MODERATE	nonsynonymous_codon ; M179T	Average:58.224; most accessible tissue: Zhenshan97 young leaf, score: 86.383	unknown	unknown	TOLERATED	0.41
vg1012696203	T -> DEL	LOC_Os10g24700.1	N	frameshift_variant	Average:58.224; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012696203	1.48E-06	NA	mr1100	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
vg1012696203	NA	9.58E-07	mr1100	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
vg1012696203	NA	2.62E-09	mr1191	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
vg1012696203	NA	4.01E-06	mr1613	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
vg1012696203	NA	6.45E-09	mr1644	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
vg1012696203	NA	1.13E-06	mr1815	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
vg1012696203	NA	3.42E-10	mr1905	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
vg1012696203	NA	6.30E-06	mr1446_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
vg1012696203	NA	6.06E-07	mr1662_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