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Detailed information for vg1214632415:

Variant ID: vg1214632415 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 14632415
Reference Allele: CAAlternative Allele: GA,CAAAA,CAA,CAAA,C,CAAAAA
Primary Allele: CASecondary Allele: GA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTGTTGGCAAAGCTGCTACACTCGCACTGCACAAGCTGAAGCTGCTGCTACTTGCATGAGAGGAATTCATCACAGATTCACAGATCTACCACACATG[CA/GA,CAAAA,CAA,CAAA,C,CAAAAA]
AAAAAAAAAAAAACAAATGAATAAGGAGCACCACAACAGCACAACTCGATGTGAATGAGGAGCACAACTAGCTTTCCAAATGAAATGCACTCCGACGAAC

Reverse complement sequence

GTTCGTCGGAGTGCATTTCATTTGGAAAGCTAGTTGTGCTCCTCATTCACATCGAGTTGTGCTGTTGTGGTGCTCCTTATTCATTTGTTTTTTTTTTTTT[TG/TC,TTTTG,TTG,TTTG,G,TTTTTG]
CATGTGTGGTAGATCTGTGAATCTGTGATGAATTCCTCTCATGCAAGTAGCAGCAGCTTCAGCTTGTGCAGTGCGAGTGTAGCAGCTTTGCCAACAAACC

Allele Frequencies:

Populations Population SizeFrequency of CA(primary allele) Frequency of GA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.10% 10.70% 25.05% 21.27% CAA: 3.05%; CAAA: 1.71%; CAAAA: 0.87%; C: 0.17%; CAAAAA: 0.06%
All Indica  2759 19.00% 3.40% 34.65% 34.51% CAA: 4.42%; CAAA: 2.25%; CAAAA: 1.49%; C: 0.18%; CAAAAA: 0.11%
All Japonica  1512 60.40% 21.80% 12.83% 2.38% CAA: 1.26%; CAAA: 1.12%; C: 0.20%
Aus  269 77.30% 19.00% 2.23% 0.74% CAA: 0.37%; CAAA: 0.37%
Indica I  595 14.50% 0.00% 43.19% 36.81% CAAAA: 3.36%; CAAA: 1.34%; CAAAAA: 0.50%; CAA: 0.34%
Indica II  465 14.60% 11.20% 38.92% 32.04% CAA: 2.15%; CAAA: 0.65%; CAAAA: 0.43%
Indica III  913 20.40% 2.60% 24.97% 39.54% CAA: 7.78%; CAAA: 3.61%; CAAAA: 0.55%; C: 0.55%
Indica Intermediate  786 23.30% 2.40% 36.90% 28.37% CAA: 4.96%; CAAA: 2.29%; CAAAA: 1.78%
Temperate Japonica  767 83.40% 3.10% 9.26% 3.39% CAA: 0.65%; CAAA: 0.13%
Tropical Japonica  504 25.20% 51.00% 17.06% 1.79% CAAA: 2.78%; CAA: 1.98%; C: 0.20%
Japonica Intermediate  241 61.00% 19.90% 15.35% 0.41% CAA: 1.66%; C: 0.83%; CAAA: 0.83%
VI/Aromatic  96 66.70% 19.80% 3.12% 9.38% CAA: 1.04%
Intermediate  90 50.00% 13.30% 27.78% 6.67% CAA: 1.11%; CAAA: 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
vg1214632415 CA -> C LOC_Os12g25350.1 downstream_gene_variant ; 2053.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> C LOC_Os12g25370.1 downstream_gene_variant ; 2039.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> C LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAA LOC_Os12g25350.1 downstream_gene_variant ; 2054.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAA LOC_Os12g25370.1 downstream_gene_variant ; 2038.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAA LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAAA LOC_Os12g25350.1 downstream_gene_variant ; 2054.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAAA LOC_Os12g25370.1 downstream_gene_variant ; 2038.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAAA LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> GA LOC_Os12g25350.1 downstream_gene_variant ; 2052.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> GA LOC_Os12g25370.1 downstream_gene_variant ; 2040.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> GA LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAA LOC_Os12g25350.1 downstream_gene_variant ; 2054.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAA LOC_Os12g25370.1 downstream_gene_variant ; 2038.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAA LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAA LOC_Os12g25350.1 downstream_gene_variant ; 2054.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAA LOC_Os12g25370.1 downstream_gene_variant ; 2038.0bp to feature; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> CAAAA LOC_Os12g25360.1 intron_variant ; MODIFIER silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 N N N N
vg1214632415 CA -> DEL N N silent_mutation Average:79.904; most accessible tissue: Zhenshan97 flower, score: 86.342 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)
vg1214632415 CA C 0.05 0.06 0.06 0.07 0.04 0.05
vg1214632415 CA CAA -0.05 0.0 0.02 -0.05 -0.07 -0.1
vg1214632415 CA CAAA -0.19 -0.03 -0.04 -0.18 -0.21 -0.28
vg1214632415 CA CAAAA -0.17 0.01 -0.03 -0.18 -0.19 -0.26
vg1214632415 CA CAAAA* -0.17 -0.04 -0.04 -0.2 -0.16 -0.16
vg1214632415 CA GA 0.03 0.01 0.01 0.03 0.03 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214632415 NA 5.14E-17 mr1016 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
vg1214632415 NA 6.13E-14 mr1017 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
vg1214632415 NA 6.92E-18 mr1022 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
vg1214632415 NA 1.89E-12 mr1023 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
vg1214632415 NA 1.05E-16 mr1055 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
vg1214632415 NA 1.08E-19 mr1079 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
vg1214632415 NA 3.13E-07 mr1082 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
vg1214632415 NA 1.54E-07 mr1083 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
vg1214632415 NA 3.39E-07 mr1085 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
vg1214632415 NA 5.89E-10 mr1093 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
vg1214632415 NA 5.40E-07 mr1103 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
vg1214632415 NA 9.84E-06 mr1107 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
vg1214632415 NA 1.86E-13 mr1132 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
vg1214632415 NA 3.97E-14 mr1142 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
vg1214632415 NA 7.83E-16 mr1178 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
vg1214632415 NA 3.13E-08 mr1226 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
vg1214632415 NA 7.86E-06 mr1235 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
vg1214632415 NA 3.44E-06 mr1257 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
vg1214632415 6.94E-06 1.89E-06 mr1284 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
vg1214632415 NA 3.30E-09 mr1301 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
vg1214632415 NA 3.57E-18 mr1390 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
vg1214632415 NA 9.41E-08 mr1408 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
vg1214632415 NA 2.27E-10 mr1410 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
vg1214632415 NA 3.87E-08 mr1411 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
vg1214632415 NA 1.08E-08 mr1489 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
vg1214632415 NA 1.59E-17 mr1490 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
vg1214632415 NA 3.15E-13 mr1491 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
vg1214632415 6.28E-06 6.29E-06 mr1499 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
vg1214632415 NA 2.10E-13 mr1546 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
vg1214632415 NA 4.56E-08 mr1560 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
vg1214632415 NA 1.39E-06 mr1599 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
vg1214632415 5.54E-07 5.53E-07 mr1605 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
vg1214632415 5.76E-07 3.33E-08 mr1727 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
vg1214632415 NA 1.24E-06 mr1756 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
vg1214632415 NA 7.02E-07 mr1805 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
vg1214632415 1.94E-06 1.94E-06 mr1840 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
vg1214632415 1.72E-06 1.71E-06 mr1856 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
vg1214632415 3.74E-06 3.34E-07 mr1856 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
vg1214632415 1.54E-06 5.44E-06 mr1898 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
vg1214632415 NA 8.85E-06 mr1949 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
vg1214632415 NA 6.42E-20 mr1022_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
vg1214632415 NA 8.90E-13 mr1023_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
vg1214632415 NA 4.57E-18 mr1055_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
vg1214632415 NA 3.11E-19 mr1079_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
vg1214632415 NA 2.19E-09 mr1093_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
vg1214632415 NA 1.41E-14 mr1132_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
vg1214632415 NA 2.24E-21 mr1178_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
vg1214632415 NA 9.23E-09 mr1235_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
vg1214632415 NA 1.88E-07 mr1243_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
vg1214632415 NA 1.90E-20 mr1390_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
vg1214632415 NA 5.70E-15 mr1410_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
vg1214632415 NA 8.49E-09 mr1489_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
vg1214632415 NA 5.15E-19 mr1490_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
vg1214632415 NA 4.29E-11 mr1546_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
vg1214632415 NA 2.42E-06 mr1580_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
vg1214632415 NA 3.20E-08 mr1805_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