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Detailed information for vg0506631795:

Variant ID: vg0506631795 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6631795
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGGCCGGATCGATCAAAGTTCTGGTACTATGCTCACGGTGGAACGCTTAACCCAGTTGATGGCTCCCTTGTCTTCGGCGATCAGATACGCGAGGCTG[C/T]
CAGTCGACTAACGGACGCAGTGGTAGCCTCTTCTTAGGGCACATTCCGACCCGACAGAGAGAAGGATGAGCTGTCACTCGCCCTTCAGACTCCAAAGCAT

Reverse complement sequence

ATGCTTTGGAGTCTGAAGGGCGAGTGACAGCTCATCCTTCTCTCTGTCGGGTCGGAATGTGCCCTAAGAAGAGGCTACCACTGCGTCCGTTAGTCGACTG[G/A]
CAGCCTCGCGTATCTGATCGCCGAAGACAAGGGAGCCATCAACTGGGTTAAGCGTTCCACCGTGAGCATAGTACCAGAACTTTGATCGATCCGGCCATTT

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	65.60%	34.20%	0.23%	0.00%	NA
All Indica	2759	61.30%	38.40%	0.29%	0.00%	NA
All Japonica	1512	65.30%	34.70%	0.07%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	89.20%	10.80%	0.00%	0.00%	NA
Indica II	465	57.00%	42.80%	0.22%	0.00%	NA
Indica III	913	38.20%	61.20%	0.55%	0.00%	NA
Indica Intermediate	786	69.50%	30.30%	0.25%	0.00%	NA
Temperate Japonica	767	94.30%	5.70%	0.00%	0.00%	NA
Tropical Japonica	504	24.60%	75.40%	0.00%	0.00%	NA
Japonica Intermediate	241	58.10%	41.50%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	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
vg0506631795	C -> T	LOC_Os05g11680-LOC_Os05g11700	intergenic_region ; MODIFIER	silent_mutation	Average:57.757; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506631795	NA	7.33E-14	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0506631795	2.16E-08	NA	mr1039	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
vg0506631795	4.65E-07	1.33E-14	mr1039	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
vg0506631795	NA	1.44E-06	mr1050	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
vg0506631795	NA	2.84E-07	mr1272	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
vg0506631795	NA	5.80E-06	mr1629	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
vg0506631795	NA	3.59E-09	mr1632	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
vg0506631795	NA	1.30E-06	mr1887	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
vg0506631795	1.18E-08	NA	mr1039_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
vg0506631795	5.73E-08	8.69E-18	mr1039_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
vg0506631795	NA	1.35E-08	mr1347_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
vg0506631795	NA	8.19E-06	mr1383_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
vg0506631795	NA	2.92E-06	mr1498_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
vg0506631795	NA	1.40E-06	mr1629_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
vg0506631795	5.81E-06	NA	mr1632_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
vg0506631795	7.02E-07	1.19E-15	mr1632_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
vg0506631795	NA	2.29E-14	mr1769_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