Additional file 1: of Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

Supplementary material. S1. Library details and depth of coverage per bird/line alignment to Galgal4. S2. Individual integrations per bird/line, sequence coverage at interval in Galgal4, and sequence coverage of EAV-HP LTR at the interval site. S3. Summary of integration site interval presence/absence per bird/line. S4. Summary of distribution of intervals. S5. Distribution of intervals relative to chromosome length. S6. Intervals and their nearest transcripts (Ensembl, Galgal4.78.gtf). S7. BLAT results of EAV-HP LTR to Galgal4. S8a. Intervals at high frequency (≥0.9) across all birds/lines. S8b. BLAT results of EAV-HP (GenBank:KC632578) to Galgal4. S9. Intervals at high frequency (≥0.8) in Ethiopian chickens from one region, and low frequency (≤0.2) in the chickens from the other region. S10. Integration site breakpoints identified near to genes in functional annotation enriched clusters. S11a. Functional annotation clustering of protein-coding genes within 5 kb of intervals. S11b. gProfiler g:GOSt analysis of genes within 5 kb of intervals. S12a. REVIGO Biological Process GO term summary of genes within 5 kb of intervals. S12b. REVIGO Cellular Component GO term summary of genes within 5 kb of intervals. S12c. REVIGO Molecular Function GO term summary of genes within 5 kb of intervals. (HTML 8512 kb)