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Table 3 Predicted consequence types of variants by prevalence level

From: Rare and population-specific functional variation across pig lines

Consequence type Percentage of variants (%) by prevalence level r
1 2 3 4 5 6 7 8 9 Total
Loss-of-functiona 0.061 0.035 0.026 0.021 0.019 0.017 0.019 0.018 0.019 0.032 − .76b
 Splice acceptor/donor 0.038 0.023 0.014 0.010 0.009 0.007 0.008 0.008 0.008 0.018 − .79b
 Stop-gain 0.014 0.009 0.008 0.008 0.007 0.007 0.007 0.006 0.006 0.009 − .82b
 Stop-loss 0.005 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.003 0.003 − .36
 Start-loss 0.004 0.002 0.002 0.002 0.001 0.001 0.002 0.002 0.002 0.002 − .47
Frameshift indel 0.014 0.017 0.019 0.021 0.020 0.021 0.024 0.032 0.055 0.027 + .81b
In-frame indel 0.005 0.008 0.009 0.008 0.008 0.008 0.007 0.007 0.005 0.006 − .23
Missense 0.556 0.378 0.355 0.340 0.344 0.336 0.319 0.306 0.325 0.393 − .73b
 Deleterious 0.201 0.092 0.074 0.069 0.064 0.062 0.054 0.048 0.040 0.096 − .78b
 Tolerated 0.223 0.170 0.165 0.165 0.173 0.167 0.161 0.159 0.177 0.183 − .52
Splice region 0.105 0.098 0.088 0.081 0.083 0.081 0.080 0.081 0.085 0.090 − .76b
Synonymous 0.240 0.313 0.334 0.348 0.355 0.353 0.337 0.331 0.353 0.316  + .65
Untranslated regions 2.300 2.252 2.257 2.191 2.146 2.156 2.093 2.089 2.061 2.180 − .98b
 Promoter + 5’ UTR 0.879 0.825 0.812 0.812 0.787 0.813 0.759 0.766 0.759 0.810 − .90b
 3’ UTR 1.421 1.427 1.445 1.378 1.359 1.343 1.334 1.322 1.302 1.370 − .94b
Non-coding transcript exon 0.104 0.113 0.107 0.113 0.128 0.118 0.105 0.109 0.117 0.111  + .25
Intronic 47.744 47.571 47.634 47.162 46.513 46.709 46.701 46.355 46.132 46.981 − .95b
Upstream of gene 3.062 3.066 3.075 3.041 3.083 3.056 2.929 2.943 2.936 3.015 − .81b
Downstream of gene 2.660 2.679 2.740 2.747 2.746 2.705 2.700 2.707 2.676 2.692 + .04
Intergenic 43.148 43.468 43.355 43.927 44.553 44.439 44.687 45.021 45.235 44.154 + .97b
  1. The most severe consequence of each variant was used. The main Sequence Ontology (SO) terms are shown in order of severity (more severe to less severe) as estimated by Ensembl Variant Effect Predictor. The correlation (r) between the percentage of variants of each consequence type and prevalence is reported
  2. In bold, categories that will be analysed in the next sections
  3. aIf frameshift indels were included in this category: r = −.06 (P > 0.05)
  4. bSignificant correlation (P < 0.05)