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Detailed information for vg0107081953:

Variant ID: vg0107081953 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 7081953
Reference Allele: GAlternative Allele: GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC,C,GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA,GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC,GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA,GGT
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTGCCGTGCAGAGTTGTAGGCAATCATTGGTTGGCGTTGATGGACCGCGTTGGTTTGATACAGCCAATGAAGGCTGTTTACCAGCAGTCCTGCACACG[G/GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC,C,GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA,GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC,GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA,GGT]
CGGAGTTGTTGATCATCTCGCTGACAGTGACAGCCCTTGCAGCAGGTGCCTCTTCTTCTCCATCTCCATCCATCAACAGCAGCAGCGGCGGCGGCGCCGC

Reverse complement sequence

GCGGCGCCGCCGCCGCTGCTGCTGTTGATGGATGGAGATGGAGAAGAAGAGGCACCTGCTGCAAGGGCTGTCACTGTCAGCGAGATGATCAACAACTCCG[C/GTTTCCATTTTTCAGTGTAGTATCGTTGACTGGCGCATGACCAATTCATTGACC,G,TTTCCATTTTTCAGTGTAGTATCGTTGACTGGCGCATGACCAATTCATTGACC,GTTTCCATTTTTCAGTGTAGTATCGTTGACTGGCGCGTGACCAATTCATTGACC,TTTCCATTTTTCAGTGTAGTATCGTTGACTGGCGCGTGACCAATTCATTGACC,ACC]
CGTGTGCAGGACTGCTGGTAAACAGCCTTCATTGGCTGTATCAAACCAACGCGGTCCATCAACGCCAACCAATGATTGCCTACAACTCTGCACGGCAGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.40% 5.50% 39.80% 9.14% GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.74%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.42%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.78%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.68%; GGT: 0.57%
All Indica  2759 13.30% 7.40% 56.32% 15.04% GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 2.97%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.96%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 1.34%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.94%; GGT: 0.72%
All Japonica  1512 76.30% 3.00% 18.65% 0.66% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.79%; GGT: 0.33%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.33%
Aus  269 97.40% 0.00% 1.49% 0.37% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.37%; GGT: 0.37%
Indica I  595 6.10% 3.40% 73.11% 14.12% GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.51%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.84%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.50%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.34%; GGT: 0.17%
Indica II  465 11.00% 8.40% 63.66% 12.26% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.94%; GGT: 1.08%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.65%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.65%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.43%
Indica III  913 17.70% 10.10% 38.77% 18.73% GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 5.81%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 3.40%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 2.85%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 1.64%; GGT: 0.99%
Indica Intermediate  786 15.10% 6.60% 59.67% 13.10% GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 2.16%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.40%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.76%; GGT: 0.64%; GGTCAATGAATTGGTCACGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.51%
Temperate Japonica  767 96.90% 0.30% 2.35% 0.13% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.26%; GGT: 0.13%
Tropical Japonica  504 40.90% 7.90% 45.83% 1.79% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 1.79%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 0.99%; GGT: 0.79%
Japonica Intermediate  241 84.60% 1.20% 13.69% 0.00% GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAAC: 0.41%
VI/Aromatic  96 92.70% 2.10% 5.21% 0.00% NA
Intermediate  90 42.20% 8.90% 40.00% 6.67% GGT: 1.11%; GGTCAATGAATTGGTCATGCGCCAGTCAACGATACTACACTGAAAAATGGAAA: 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
vg0107081953 G -> GGTCAATGAATTGGTCATGCGCCAGTCAAC GATACTACACTGAAAAATGGAAAC LOC_Os01g12790.1 frameshift_variant&stop_gained ; p.Ala159fs; HIGH frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 N N N N
vg0107081953 G -> GGTCAATGAATTGGTCATGCGCCAGTCAAC GATACTACACTGAAAAATGGAAA LOC_Os01g12790.1 frameshift_variant&stop_gained ; p.Ala159fs; HIGH frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 N N N N
vg0107081953 G -> GGTCAATGAATTGGTCACGCGCCAGTCAAC GATACTACACTGAAAAATGGAAA LOC_Os01g12790.1 frameshift_variant&stop_gained ; p.Ala159fs; HIGH frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 N N N N
vg0107081953 G -> C LOC_Os01g12790.1 missense_variant ; p.Ala159Pro; MODERATE nonsynonymous_codon ; A159P Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 unknown unknown TOLERATED 0.06
vg0107081953 G -> GGT LOC_Os01g12790.1 frameshift_variant ; p.Ala159fs; HIGH frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 N N N N
vg0107081953 G -> GGTCAATGAATTGGTCACGCGCCAGTCAAC GATACTACACTGAAAAATGGAAAC LOC_Os01g12790.1 frameshift_variant&stop_gained ; p.Ala159fs; HIGH frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 N N N N
vg0107081953 G -> DEL LOC_Os01g12790.1 N frameshift_variant Average:87.591; most accessible tissue: Zhenshan97 root, score: 98.043 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)
vg0107081953 G C 0.0 0.01 -0.02 -0.04 -0.02 0.02
vg0107081953 G GGT 0.19 0.18 0.09 0.03 0.05 -0.1
vg0107081953 G GGTCA* -0.05 0.16 0.22 0.22 0.07 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107081953 NA 9.87E-21 mr1179 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
vg0107081953 NA 7.32E-08 mr1364 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
vg0107081953 NA 3.66E-06 mr1364 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
vg0107081953 NA 4.96E-09 mr1403 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
vg0107081953 NA 1.48E-26 mr1422 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
vg0107081953 NA 1.02E-07 mr1422 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
vg0107081953 NA 7.22E-08 mr1443 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
vg0107081953 NA 1.58E-06 mr1443 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
vg0107081953 NA 2.83E-08 mr1518 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
vg0107081953 NA 1.29E-08 mr1539 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
vg0107081953 NA 7.14E-14 mr1540 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
vg0107081953 NA 1.31E-18 mr1583 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
vg0107081953 NA 4.48E-09 mr1676 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
vg0107081953 4.28E-06 NA mr1699 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
vg0107081953 1.66E-06 2.21E-29 mr1699 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
vg0107081953 NA 9.90E-12 mr1720 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
vg0107081953 NA 1.13E-13 mr1732 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
vg0107081953 NA 1.07E-12 mr1769 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
vg0107081953 NA 2.14E-18 mr1769 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
vg0107081953 NA 5.93E-07 mr1925 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
vg0107081953 NA 1.42E-07 mr1951 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
vg0107081953 NA 2.55E-10 mr1228_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
vg0107081953 NA 2.02E-16 mr1260_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
vg0107081953 NA 4.36E-15 mr1301_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
vg0107081953 NA 1.81E-10 mr1364_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
vg0107081953 NA 1.22E-22 mr1401_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
vg0107081953 NA 2.07E-28 mr1422_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
vg0107081953 NA 4.50E-07 mr1422_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
vg0107081953 NA 2.93E-08 mr1498_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
vg0107081953 NA 1.55E-07 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
vg0107081953 NA 5.24E-18 mr1583_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
vg0107081953 9.74E-06 2.36E-11 mr1676_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
vg0107081953 NA 2.21E-22 mr1699_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
vg0107081953 NA 6.90E-15 mr1720_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
vg0107081953 6.20E-06 6.87E-10 mr1769_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
vg0107081953 NA 1.44E-15 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
vg0107081953 NA 1.68E-13 mr1850_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
vg0107081953 NA 6.35E-10 mr1916_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
vg0107081953 NA 1.08E-06 mr1925_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
vg0107081953 NA 1.61E-11 mr1993_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
vg0107081953 NA 6.40E-13 mr1993_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