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Detailed information for vg1008776633:

Variant ID: vg1008776633 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 8776633
Reference Allele: AAlternative Allele: ATACAT,G,ATACATCCTGTCTTTGAACCTTTGTAGTCCTATGCATAGTCAGTACTATAGCTCCAATCATAGCTACTAATAAAATCAGACTAGAAACC,ATTT,T
Primary Allele: ASecondary Allele: ATACATCCTGTCTTTGAACC TTTGTAGTCCTATGCATAGT CAGTACTATAGCTCCAATCA TAGCTACTAATAAAATCAGA CTAGAAACC

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CGATGTCGAAGAGTATCTCTTCTTCTCTTCTGTTCTCTTGCGAGCCGAAAGCAACTTTGATGAGGGCTTGTCCCAGAACCTGCACCGCTTCGCCTCCAAA[A/ATACAT,G,ATACATCCTGTCTTTGAACCTTTGTAGTCCTATGCATAGTCAGTACTATAGCTCCAATCATAGCTACTAATAAAATCAGACTAGAAACC,ATTT,T]
CCTCTGAGTGAAGTCGGTGCTTGAGATAATGCCAAAGTTGGCAAACCCATCTTGGCATATGTCCCGGCGAACATGACATCAGCCGAACTCCCTCCATCAA

Reverse complement sequence

TTGATGGAGGGAGTTCGGCTGATGTCATGTTCGCCGGGACATATGCCAAGATGGGTTTGCCAACTTTGGCATTATCTCAAGCACCGACTTCACTCAGAGG[T/ATGTAT,C,GGTTTCTAGTCTGATTTTATTAGTAGCTATGATTGGAGCTATAGTACTGACTATGCATAGGACTACAAAGGTTCAAAGACAGGATGTAT,AAAT,A]
TTTGGAGGCGAAGCGGTGCAGGTTCTGGGACAAGCCCTCATCAAAGTTGCTTTCGGCTCGCAAGAGAACAGAAGAGAAGAAGAGATACTCTTCGACATCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of ATACATCCTGTCTTTGAACC TTTGTAGTCCTATGCATAGT CAGTACTATAGCTCCAATCA TAGCTACTAATAAAATCAGA CTAGAAACC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.30% 1.40% 15.07% 16.84% G: 1.14%; ATACAT: 0.95%; ATTT: 0.34%; T: 0.04%
All Indica  2759 52.40% 1.80% 21.24% 21.17% G: 1.74%; ATACAT: 1.16%; ATTT: 0.43%
All Japonica  1512 80.80% 0.50% 6.94% 10.45% ATACAT: 0.79%; ATTT: 0.26%; G: 0.20%; T: 0.13%
Aus  269 82.90% 0.00% 1.12% 15.99% NA
Indica I  595 43.90% 2.90% 31.09% 18.66% G: 2.18%; ATTT: 0.67%; ATACAT: 0.67%
Indica II  465 55.90% 2.60% 16.99% 21.72% ATACAT: 1.08%; G: 0.86%; ATTT: 0.86%
Indica III  913 52.60% 0.30% 19.28% 24.21% G: 2.41%; ATACAT: 1.10%; ATTT: 0.11%
Indica Intermediate  786 56.60% 2.40% 18.58% 19.21% ATACAT: 1.65%; G: 1.15%; ATTT: 0.38%
Temperate Japonica  767 95.00% 0.50% 0.78% 3.65% NA
Tropical Japonica  504 61.90% 0.60% 17.86% 15.87% ATACAT: 2.18%; G: 0.60%; ATTT: 0.60%; T: 0.40%
Japonica Intermediate  241 74.70% 0.00% 3.73% 20.75% ATTT: 0.41%; ATACAT: 0.41%
VI/Aromatic  96 81.20% 4.20% 11.46% 2.08% G: 1.04%
Intermediate  90 76.70% 2.20% 7.78% 10.00% G: 2.22%; ATACAT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008776633 A -> G LOC_Os10g17410.1 synonymous_variant ; p.Gly621Gly; LOW synonymous_codon Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N
vg1008776633 A -> T LOC_Os10g17410.1 synonymous_variant ; p.Gly621Gly; LOW synonymous_codon Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N
vg1008776633 A -> DEL LOC_Os10g17410.1 N frameshift_variant Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N
vg1008776633 A -> ATACATCCTGTCTTTGAACCTTTGTAGTCC TATGCATAGTCAGTACTATAGCTCCAATCA TAGCTACTAATAAAATCAGACTAGAAACC LOC_Os10g17410.1 frameshift_variant ; p.Phe622fs; HIGH frameshift_variant Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N
vg1008776633 A -> ATACAT LOC_Os10g17410.1 frameshift_variant ; p.Phe622fs; HIGH frameshift_variant Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N
vg1008776633 A -> ATTT LOC_Os10g17410.1 disruptive_inframe_insertion ; p.Gly621_Phe622insAsn; MODERATE inframe_variant Average:76.156; most accessible tissue: Zhenshan97 flag leaf, score: 95.104 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1008776633 A ATACA* 0.02 0.01 -0.01 0.0 0.01 0.01
vg1008776633 A ATTT -0.01 -0.01 -0.01 -0.01 -0.01 -0.02
vg1008776633 A G 0.0 0.01 0.01 0.01 0.01 0.01
vg1008776633 A T 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008776633 1.04E-10 1.62E-52 mr1026 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
vg1008776633 4.04E-12 3.55E-28 mr1026 Ind_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
vg1008776633 NA 7.80E-09 mr1113 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
vg1008776633 NA 8.44E-09 mr1114 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
vg1008776633 NA 2.08E-08 mr1116 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
vg1008776633 1.91E-07 3.50E-17 mr1118 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
vg1008776633 1.09E-14 2.10E-31 mr1118 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
vg1008776633 NA 5.64E-07 mr1119 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
vg1008776633 3.23E-06 1.07E-08 mr1120 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
vg1008776633 NA 7.15E-07 mr1123 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
vg1008776633 1.11E-09 4.38E-49 mr1161 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
vg1008776633 3.43E-10 3.03E-25 mr1161 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
vg1008776633 NA 1.04E-06 mr1242 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
vg1008776633 NA 7.13E-08 mr1247 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
vg1008776633 NA 9.13E-15 mr1261 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
vg1008776633 NA 5.53E-10 mr1261 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
vg1008776633 2.97E-08 3.80E-23 mr1495 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
vg1008776633 2.41E-13 1.76E-32 mr1495 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
vg1008776633 NA 1.25E-10 mr1496 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
vg1008776633 4.18E-06 NA mr1794 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
vg1008776633 6.95E-07 8.01E-12 mr1794 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
vg1008776633 NA 9.92E-06 mr1917 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
vg1008776633 NA 3.48E-07 mr1936 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
vg1008776633 NA 1.27E-09 mr1108_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
vg1008776633 NA 2.69E-09 mr1113_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
vg1008776633 NA 4.64E-10 mr1114_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
vg1008776633 NA 2.02E-07 mr1117_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
vg1008776633 NA 2.07E-20 mr1118_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
vg1008776633 5.42E-11 2.25E-34 mr1118_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
vg1008776633 NA 2.46E-07 mr1119_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
vg1008776633 NA 3.02E-12 mr1120_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
vg1008776633 NA 1.17E-06 mr1123_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
vg1008776633 3.30E-09 2.21E-50 mr1161_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
vg1008776633 1.38E-08 1.47E-25 mr1161_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
vg1008776633 NA 7.37E-07 mr1212_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
vg1008776633 NA 1.47E-06 mr1233_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
vg1008776633 6.54E-06 2.43E-11 mr1247_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
vg1008776633 1.87E-06 3.03E-07 mr1258_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
vg1008776633 1.17E-07 3.02E-30 mr1495_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
vg1008776633 1.37E-11 1.17E-35 mr1495_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
vg1008776633 NA 2.78E-10 mr1496_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
vg1008776633 NA 6.10E-14 mr1794_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
vg1008776633 NA 3.02E-09 mr1936_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
vg1008776633 NA 9.78E-07 mr1961_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