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Detailed information for vg1016551649:

Variant ID: vg1016551649 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16551649
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

AACTTCGGCAAGATCTCTCTCCTTGACTCGGAGTCGGACCAGTCGGGAGAGAACTGGATCTCAGTCCCGTTTGGACTCCCAAACGCGGCTGAAAGTTACT[C/T]
CAAGACCATCTCAATCGAGTCGGCTTCAAACCACTCGGCTGAGATTGCATCTTCTCCAACGTCACCAGATCAAGATGATGGGGCTTACCCACCGATCCTG

Reverse complement sequence

CAGGATCGGTGGGTAAGCCCCATCATCTTGATCTGGTGACGTTGGAGAAGATGCAATCTCAGCCGAGTGGTTTGAAGCCGACTCGATTGAGATGGTCTTG[G/A]
AGTAACTTTCAGCCGCGTTTGGGAGTCCAAACGGGACTGAGATCCAGTTCTCTCCCGACTGGTCCGACTCCGAGTCAAGGAGAGAGATCTTGCCGAAGTT

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	20.50%	2.30%	38.28%	38.93%	NA
All Indica	2759	12.20%	1.20%	41.61%	44.94%	NA
All Japonica	1512	40.10%	4.00%	29.70%	26.26%	NA
Aus	269	0.00%	2.20%	37.17%	60.59%	NA
Indica I	595	2.70%	3.90%	36.13%	57.31%	NA
Indica II	465	14.80%	0.00%	23.66%	61.51%	NA
Indica III	913	15.90%	0.30%	56.08%	27.71%	NA
Indica Intermediate	786	13.60%	1.00%	39.57%	45.80%	NA
Temperate Japonica	767	73.80%	0.10%	10.95%	15.12%	NA
Tropical Japonica	504	2.40%	10.10%	47.22%	40.28%	NA
Japonica Intermediate	241	11.60%	3.30%	52.70%	32.37%	NA
VI/Aromatic	96	1.00%	5.20%	73.96%	19.79%	NA
Intermediate	90	26.70%	4.40%	45.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1016551649	C -> T	LOC_Os10g31590.1	missense_variant ; p.Ser62Phe; MODERATE	nonsynonymous_codon ; S62F	Average:26.974; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	benign	-0.483	TOLERATED	0.06
vg1016551649	C -> DEL	LOC_Os10g31590.1	N	frameshift_variant	Average:26.974; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016551649	NA	3.20E-13	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
vg1016551649	NA	9.01E-15	Grain_length	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
vg1016551649	NA	9.54E-06	mr1029	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
vg1016551649	NA	7.13E-09	mr1137	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
vg1016551649	NA	3.46E-06	mr1330	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
vg1016551649	NA	4.73E-37	mr1486	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
vg1016551649	NA	1.28E-14	mr1486	Jap_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
vg1016551649	NA	5.74E-07	mr1530	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
vg1016551649	NA	4.24E-06	mr1548	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
vg1016551649	NA	4.12E-07	mr1617	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
vg1016551649	NA	5.78E-06	mr1826	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
vg1016551649	NA	1.58E-06	mr1871	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
vg1016551649	NA	9.99E-12	mr1902	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
vg1016551649	NA	3.55E-06	mr1902	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
vg1016551649	NA	9.86E-07	mr1570_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