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Detailed information for vg0507091150:

Variant ID: vg0507091150 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7091150
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGAGGTGCTCAAGAAGAACATCGACACATTCGCCTGGAGCCCTGACGAGGTGGGGGGTGTTCCGGCAGATCTCATCATGCATCACCTGGCGGTCAAGC[T/C]
GGACATTAAGCCAAGAAAACAGAAGTTGCGCAAGATGTCTGCCGACCGCCAAGAAGCGGCGAAAGCCGAGGTACAAAAATTGCTCAGGGCAGGGGTAATC

Reverse complement sequence

GATTACCCCTGCCCTGAGCAATTTTTGTACCTCGGCTTTCGCCGCTTCTTGGCGGTCGGCAGACATCTTGCGCAACTTCTGTTTTCTTGGCTTAATGTCC[A/G]
GCTTGACCGCCAGGTGATGCATGATGAGATCTGCCGGAACACCCCCCACCTCGTCAGGGCTCCAGGCGAATGTGTCGATGTTCTTCTTGAGCACCTCTAG

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	55.90%	18.90%	3.39%	21.77%	NA
All Indica	2759	78.50%	0.70%	4.28%	16.56%	NA
All Japonica	1512	10.30%	56.70%	1.85%	31.08%	NA
Aus	269	94.40%	0.40%	2.23%	2.97%	NA
Indica I	595	87.10%	0.50%	3.36%	9.08%	NA
Indica II	465	61.90%	1.70%	8.17%	28.17%	NA
Indica III	913	78.50%	0.30%	3.94%	17.20%	NA
Indica Intermediate	786	81.80%	0.50%	3.05%	14.63%	NA
Temperate Japonica	767	1.20%	91.10%	0.52%	7.17%	NA
Tropical Japonica	504	20.40%	9.70%	4.37%	65.48%	NA
Japonica Intermediate	241	18.30%	45.60%	0.83%	35.27%	NA
VI/Aromatic	96	24.00%	0.00%	3.12%	72.92%	NA
Intermediate	90	48.90%	18.90%	5.56%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507091150	T -> DEL	LOC_Os05g12340.1	N	frameshift_variant	Average:24.478; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0507091150	T -> C	LOC_Os05g12340.1	missense_variant ; p.Leu196Pro; MODERATE	nonsynonymous_codon ; L196S	Average:24.478; most accessible tissue: Minghui63 panicle, score: 50.413	benign	1.361	TOLERATED	0.12
vg0507091150	T -> C	LOC_Os05g12340.1	missense_variant ; p.Leu196Pro; MODERATE	nonsynonymous_codon ; L196P	Average:24.478; most accessible tissue: Minghui63 panicle, score: 50.413	benign	-0.378	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507091150	NA	3.26E-42	Grain_thickness	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
vg0507091150	NA	1.54E-13	Grain_thickness	Jap_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
vg0507091150	NA	1.20E-06	mr1308	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
vg0507091150	NA	1.69E-06	mr1401	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
vg0507091150	NA	3.37E-27	mr1423	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
vg0507091150	NA	2.76E-08	mr1549	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
vg0507091150	7.47E-12	3.71E-12	mr1593	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
vg0507091150	2.05E-09	2.66E-26	mr1593	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
vg0507091150	NA	7.10E-12	mr1741	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
vg0507091150	NA	2.97E-24	mr1862	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
vg0507091150	NA	2.25E-07	mr1916	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
vg0507091150	NA	3.78E-51	mr1093_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
vg0507091150	NA	1.50E-10	mr1093_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
vg0507091150	NA	3.76E-09	mr1235_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
vg0507091150	NA	2.99E-06	mr1423_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
vg0507091150	8.70E-09	1.26E-11	mr1593_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
vg0507091150	3.78E-14	1.04E-37	mr1593_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
vg0507091150	NA	2.09E-13	mr1800_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