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Detailed information for vg0624612242:

Variant ID: vg0624612242 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24612242
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTTGTGGCCCGTCACGGATAACCATCATCCGTGACGTGCACCAACTTGAGGCCCGTTTGAGATAGCAACTAGGTCCGTCACAGATGACTCATCAATGA[C/T]
GGGCTATATACTTAATCTCTATCGGGCATTAACTAAAACCCGTCACCGATGACTATTTTTCATTTTTTATATGAAATTTTTATATTTGTAAGTTGAACTA

Reverse complement sequence

TAGTTCAACTTACAAATATAAAAATTTCATATAAAAAATGAAAAATAGTCATCGGTGACGGGTTTTAGTTAATGCCCGATAGAGATTAAGTATATAGCCC[G/A]
TCATTGATGAGTCATCTGTGACGGACCTAGTTGCTATCTCAAACGGGCCTCAAGTTGGTGCACGTCACGGATGATGGTTATCCGTGACGGGCCACAACTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.80%	44.90%	0.25%	0.11%	NA
All Indica	2759	90.50%	8.90%	0.36%	0.18%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	14.90%	85.10%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.00%	0.34%	NA
Indica II	465	91.40%	7.70%	0.43%	0.43%	NA
Indica III	913	87.60%	12.20%	0.22%	0.00%	NA
Indica Intermediate	786	86.80%	12.30%	0.76%	0.13%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	42.20%	55.60%	2.22%	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
vg0624612242	C -> T	LOC_Os06g41140-LOC_Os06g41150	intergenic_region ; MODIFIER	silent_mutation	Average:27.722; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0624612242	C -> DEL	N	N	silent_mutation	Average:27.722; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624612242	6.88E-07	8.35E-08	mr1011	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
vg0624612242	NA	4.40E-19	mr1077	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
vg0624612242	NA	2.56E-48	mr1125	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
vg0624612242	NA	4.44E-08	mr1124_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
vg0624612242	NA	2.31E-20	mr1531_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
vg0624612242	NA	5.16E-07	mr1531_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
vg0624612242	NA	8.93E-06	mr1600_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