Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages

Table 1 Summary statistics of the identified variants using the respective methods, from the bovine genome using DNA chip and from the transcriptome of the macrophages using RNA-seq

Genotyping methods (counts)	DNA chip	RNAseq	Merge
Variants processed
SNPs	591,220	814,168	1,356,248
Insertions	0	50,272	50,272
Deletions	0	43,007	43,007
Categories
MISSENSE	2203	17,644	18,788
NONSENSE	4	96	99
SILENT	4473	25,954	27,879
Effects by impact
HIGH	33	2435	2459
LOW	5109	28,359	30,762
MODERATE	2202	17,996	19,139
MODIFIER	664.774	1,053,336	1,655,791
Effects by type and region
3_prime_UTR_variant	2110	19,914	20,494
5_prime_UTR_premature_start_codon	58	459	483
5_prime_UTR_truncation	0	1	1
5_prime_UTR_variant	318	3506	3648
bidirectional_gene_fusion	0	1	1
conservative_inframe_deletion	0	103	103
conservative_inframe_insertion	0	77	77
disruptive_inframe_deletion	0	137	137
disruptive_inframe_insertion	0	90	90
downstream_gene_variant	28,694	146,242	166,616
exon_loss_variant	0	1	1
frameshift_variant	0	1754	1754
gene_fusion	0	1	1
initiator_codon_variant	0	2	2
intergenic_region	401,382	251,262	640,031
intragenic_variant	0	2	2
intron_variant	205,303	557,864	727,911
missense_variant	2202	17,628	18,771
non_coding_transcript_exon_variant	200	1611	1781
non_coding_transcript_variant	0	10	10
splice_acceptor_variant	12	496	504
splice_donor_variant	16	590	602
splice_region_variant	735	3146	3704
start_lost	1	12	13
stop_gained	4	118	121
stop_lost	0	12	12
stop_retained_variant	2	18	18
synonymous_variant	4471	25,936	27,861
upstream_gene_variant	27,358	75,567	98,406

ISSN: 1471-2164