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Detailed information for vg0141375724:

Variant ID: vg0141375724 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41375724
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: 0.02, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TCAACATCAGGTACATCGCCGTCGGGAACGAGGTGTCCGGCGACGCCACGCGGAGCATCCTCCCGGCCATGGAGAACCTCACCAAGGCGCTGTCCGCGGC[C/T]
GGCTTCGGCAAGATCAAGGTGTCCACGGCCGTCAAGATGGACGTGCTCGGCACCTCGTCGCCGCCCTCCGGCGGCGAGTTCAGCGACGCCGCCGTCATGG

Reverse complement sequence

CCATGACGGCGGCGTCGCTGAACTCGCCGCCGGAGGGCGGCGACGAGGTGCCGAGCACGTCCATCTTGACGGCCGTGGACACCTTGATCTTGCCGAAGCC[G/A]
GCCGCGGACAGCGCCTTGGTGAGGTTCTCCATGGCCGGGAGGATGCTCCGCGTGGCGTCGCCGGACACCTCGTTCCCGACGGCGATGTACCTGATGTTGA

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	67.20%	32.30%	0.11%	0.40%	NA
All Indica	2759	45.70%	53.60%	0.14%	0.54%	NA
All Japonica	1512	98.40%	1.50%	0.00%	0.13%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	83.20%	16.60%	0.00%	0.17%	NA
Indica II	465	12.90%	86.00%	0.00%	1.08%	NA
Indica III	913	35.50%	64.50%	0.00%	0.00%	NA
Indica Intermediate	786	48.60%	49.70%	0.51%	1.15%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.40%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	25.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141375724	C -> T	LOC_Os01g71410.1	synonymous_variant ; p.Ala173Ala; LOW	synonymous_codon	Average:70.818; most accessible tissue: Zhenshan97 flower, score: 73.946	N	N	N	N
vg0141375724	C -> DEL	LOC_Os01g71410.1	N	frameshift_variant	Average:70.818; most accessible tissue: Zhenshan97 flower, score: 73.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141375724	NA	3.04E-16	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
vg0141375724	NA	2.57E-16	Grain_length	Ind_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
vg0141375724	NA	7.10E-08	Grain_thickness	Ind_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
vg0141375724	NA	8.73E-14	Grain_width	Ind_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
vg0141375724	NA	2.91E-06	mr1399	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
vg0141375724	NA	3.12E-07	mr1458	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
vg0141375724	NA	6.27E-06	mr1974	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
vg0141375724	NA	6.58E-07	mr1974	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
vg0141375724	NA	1.78E-09	mr1319_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
vg0141375724	NA	6.02E-09	mr1322_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
vg0141375724	NA	1.40E-13	mr1330_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
vg0141375724	NA	1.12E-07	mr1458_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
vg0141375724	NA	2.23E-07	mr1527_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