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Detailed information for vg1224760800:

Variant ID: vg1224760800 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24760800
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, C: 0.20, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGAGTTTGGATGGGCCCTGCGACCGCCTATGCGGCTTCCGGATTCACCTAGGCACGAGAGGGGACTGCCCGCTGCCTTGCGAGGAGTGGGGGTGAAAC[T/C]
TGAGGTGTGGTGTGCTTGGTTAGAGGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCGGTATATCGTGGTGGCATGTCGGCGCACGGAAACGTGTC

Reverse complement sequence

GACACGTTTCCGTGCGCCGACATGCCACCACGATATACCGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCCTCTAACCAAGCACACCACACCTCA[A/G]
GTTTCACCCCCACTCCTCGCAAGGCAGCGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCGGAAGCCGCATAGGCGGTCGCAGGGCCCATCCAAACTCCAT

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	68.70%	30.90%	0.49%	0.00%	NA
All Indica	2759	93.00%	6.30%	0.72%	0.00%	NA
All Japonica	1512	22.60%	77.30%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.60%	0.50%	2.86%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	87.40%	12.50%	0.11%	0.00%	NA
Indica Intermediate	786	93.00%	6.70%	0.25%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	56.90%	42.90%	0.20%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	86.50%	1.04%	0.00%	NA
Intermediate	90	63.30%	35.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224760800	T -> C	LOC_Os12g40050.1	missense_variant ; p.Leu34Pro; MODERATE	nonsynonymous_codon ; L34P	Average:18.31; most accessible tissue: Zhenshan97 flag leaf, score: 30.355	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224760800	2.10E-06	NA	mr1124	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
vg1224760800	NA	6.11E-06	mr1218_2	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
vg1224760800	NA	3.57E-16	mr1334_2	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
vg1224760800	NA	6.86E-08	mr1422_2	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
vg1224760800	NA	1.04E-06	mr1850_2	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
vg1224760800	NA	1.22E-07	mr1991_2	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