Table 5 Results of variant effect prediction for the production traits average daily gain (ADG), back fat thickness (BFT), meat to fat ratio (MFR), and carcass length (CRCL). Bonferroni-corrected variants were analyzed
Predicted effectADGADG %BFTBFT %MFRMFR %CRCLCRCL %
Missense variant20.1580962*0.6523*580.1893787*0.4750*
Frameshift variant00000*0*6*0.0036*
Start lost0010.00070000
Stop gained00000010.0006
Inframe deletion001*0.0007*0020.0012
Intron variant93673.933611681579.209021556*70.3525*13159079.4275
5 prime UTR variant00229*0.1553*890.2905277*0.1672*
3 prime UTR variant80.63191160*0.7866*12424.05351543*0.9314*
Upstream gene variant503.94945680*3.8514*2195*7.1638*5300*3.1991*
Downstream gene variant44*3.4755*5791*3.9267*344211.23376893*4.1606*
Frameshift variant, splice region variant0020.00140000
Missense variant, splice region variant0041*0.0278*0075*0.0453*
Splice region variant, non coding transcript exon variant0020.00143*0.0098*50.0030
Splice region variant, 3 prime UTR variant003*0.0020*3*0.0098*00
Splice region variant, intron variant, non coding transcript variant002*0.0014*40.013120*0.0121*
Splice region variant, intron variant00426*0.2889*41*0.1338*489*0.2952*
Splice region variant, synonymous variant00210.014222*0.0718*28*0.0169*
Splice donor variant00360.0244*1*0.0033370.0223
Intergenic variant1098.609833182.24986442.101899095.9811
Synonymous variant0028371.9237214*0.6984*27511.6605
Intron variant, non coding transcript variant117*9.2417*96366.53391060*3.4595*5759*3.4761*
Non coding transcript exon variant00514*0.3485*660.2154200*0.1207*
Start lost, start retained variant, 5 prime UTR variant0000001*0.0006*
Total126614747730640165673