Table 5 Prediction of the effects of SNPs and InDels
From: Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset
Impact (count, percentage in Sunset) | Effect type | Count | Percentage (%) |
|---|---|---|---|
HIGH (1591, 0.2714%) | frameshift_variant | 1033 | 0.1762 |
frameshift_variant+splice_region_variant | 66 | 0.0113 | |
frameshift_variant+start_lost | 12 | 0.0020 | |
frameshift_variant+stop_gained | 9 | 0.0015 | |
frameshift_variant+stop_gained+splice_region_variant | 1 | 0.0002 | |
frameshift_variant+stop_lost | 1 | 0.0002 | |
frameshift_variant+stop_lost+splice_region_variant | 15 | 0.0026 | |
splice_acceptor_variant+intron_variant | 75 | 0.0128 | |
splice_acceptor_variant+splice_region_variant+intron_variant | 2 | 0.0003 | |
splice_donor_variant+intron_variant | 87 | 0.0148 | |
splice_donor_variant+splice_region_variant+intron_variant | 1 | 0.0002 | |
start_lost | 24 | 0.0041 | |
start_lost+splice_region_variant | 1 | 0.0002 | |
stop_gained | 185 | 0.0316 | |
stop_gained+disruptive_inframe_insertion | 1 | 0.0002 | |
stop_gained+splice_region_variant | 6 | 0.0010 | |
stop_lost | 23 | 0.0039 | |
stop_lost+inframe_insertion+splice_region_variant | 1 | 0.0002 | |
stop_lost+splice_region_variant | 48 | 0.0082 | |
MODERATE (7533, 1.2849%) | missense_variant+splice_region_variant | 130 | 0.0222 |
disruptive_inframe_deletion | 3 | 0.0005 | |
disruptive_inframe_insertion | 7 | 0.0012 | |
inframe_deletion | 17 | 0.0029 | |
inframe_insertion | 22 | 0.0038 | |
missense_variant | 7354 | 1.2544 | |
LOW (6114, 1.0429%) | initiator_codon_variant | 9 | 0.0015 |
splice_region_variant+intron_variant | 833 | 0.1421 | |
splice_region_variant+stop_retained_variant | 13 | 0.0022 | |
splice_region_variant+synonymous_variant | 100 | 0.0171 | |
stop_retained_variant | 4 | 0.0007 | |
synonymous_variant | 5155 | 0.8793 | |
MODIFIER (571,039, 97.4009%) | downstream_gene_variant | 128,197 | 21.8663 |
intergenic_region | 278,076 | 47.4308 | |
intron_variant | 36,054 | 6.1497 | |
upstream_gene_variant | 128,712 | 21.9541 |